3BIW | pdb_00003biw

Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d3biwh1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	Ligand-binding domain of neurexin 1beta	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G	d3biwg1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	Ligand-binding domain of neurexin 1beta	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d3biwf1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	Ligand-binding domain of neurexin 1beta	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d3biwe1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Laminin G-like module	Ligand-binding domain of neurexin 1beta	Norway rat (Rattus norvegicus ) [TaxId: 10116 ], Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Laminin_G_1	e3biwH1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)
G	Laminin_G_1	e3biwG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)
F	Laminin_G_1	e3biwF1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)
E	Laminin_G_1	e3biwE1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Laminin_G_1	ECOD (1.6)
D	COesterase	e3biwD1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
C	COesterase	e3biwC1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
B	COesterase	e3biwB1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)
A	COesterase	e3biwA1	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: COesterase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
G	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
C	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
B	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
A	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F, G, H	PF02210	Laminin G domain (Laminin_G_2)	Laminin G domain	This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	Neurexin-1-beta	channel regulator activity ion channel regulator activity calcium channel regulator activity molecular function regulator activity transporter regulator activity protein-containing complex binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding channel regulator activity ion channel regulator activity calcium channel regulator activity molecular function regulator activity transporter regulator activity protein-containing complex binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor binding fibroblast growth factor receptor binding growth factor receptor binding type 1 fibroblast growth factor receptor binding cell adhesion molecule binding acetylcholine receptor binding neuroligin family protein binding	cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling behavior learning learning or memory cognition imitative learning auditory behavior vocal learning learned vocalization behavior or vocal learning response to mechanical stimulus response to external stimulus mechanosensory behavior response to auditory stimulus observational learning response to abiotic stimulus regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process cellular component organization positive regulation of developmental process multicellular organism development anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis system development developmental process nervous system development developmental maturation synapse maturation regulation of synapse organization regulation of synapse maturation cell junction organization positive regulation of synapse maturation regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process cellular localization postsynaptic membrane assembly membrane biogenesis cellular component biogenesis localization cellular component assembly cell junction assembly receptor clustering intracellular protein localization postsynaptic membrane organization membrane organization postsynapse organization postsynapse assembly neuroligin clustering involved in postsynaptic membrane assembly localization within membrane protein localization to membrane membrane assembly macromolecule localization synapse assembly organelle organization postsynaptic density protein 95 clustering postsynaptic density organization postsynaptic specialization organization regulation of behavior regulation of grooming behavior grooming behavior regulation of postsynaptic specialization assembly organelle assembly postsynaptic specialization assembly regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly response to fibroblast growth factor cellular response to growth factor stimulus positive regulation of fibroblast growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus enzyme-linked receptor protein signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus fibroblast growth factor receptor signaling pathway response to growth factor cellular response to fibroblast growth factor stimulus regulation of fibroblast growth factor receptor signaling pathway startle response regulation of response to external stimulus neuromuscular process negative regulation of response to stimulus negative regulation of biological process prepulse inhibition negative regulation of response to external stimulus regulation of excitatory synapse assembly regulation of synapse assembly regulation of postsynaptic density organization regulation of postsynapse organization excitatory synapse assembly regulation of cell junction assembly postsynaptic density assembly regulation of postsynaptic density assembly plasma membrane bounded cell projection organization cellular developmental process cell projection organization cell development neuron projection development generation of neurons neurogenesis neuron differentiation cell differentiation neuron development regulation of localization transport regulation of transport regulation of synaptic vesicle cycle synaptic vesicle cycle regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse establishment of localization in cell presynapse organization presynapse assembly rhythmic process circadian rhythm positive regulation of nervous system development regulation of nervous system development regulation of multicellular organismal development positive regulation of cellular component biogenesis positive regulation of cell junction assembly positive regulation of multicellular organismal process positive regulation of synapse assembly intracellular signal transduction positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic neurotransmitter secretion secretion export from cell neurotransmitter transport signal release from synapse secretion by cell signal release cell adhesion cell-cell adhesion synaptic membrane adhesion regulation of presynapse assembly regulation of presynapse organization trans-synaptic signaling, modulating synaptic transmission trans-synaptic signaling by endocannabinoid regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission trans-synaptic signaling by lipid, modulating synaptic transmission trans-synaptic signaling by lipid trans-synaptic signaling by endocannabinoid, modulating synaptic transmission adult behavior membrane docking organelle localization by membrane tethering exocytosis organelle localization vesicle docking exocytic process vesicle docking involved in exocytosis neuromuscular process controlling balance regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction phospholipase C-activating G protein-coupled receptor signaling pathway regulation of G protein-coupled receptor signaling pathway positive regulation of G protein-coupled receptor signaling pathway positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway regulation of phospholipase C-activating G protein-coupled receptor signaling pathway biological process involved in intraspecies interaction between organisms social behavior negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process vocalization behavior protein localization to synapse gephyrin clustering involved in postsynaptic density assembly protein localization to cell junction	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cell periphery membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane cell periphery presynapse synapse cell junction plasma membrane presynaptic membrane plasma membrane region synaptic membrane glutamatergic synapse somatodendritic compartment cell body neuronal cell body vesicle cell-cell junction anchoring junction filtration diaphragm slit diaphragm cell surface protein-containing complex GABA-ergic synapse presynaptic active zone membrane presynaptic active zone trans-synaptic protein complex Schaffer collateral - CA1 synapse cell projection endoplasmic reticulum cytoplasm
A, B, C, D	Neuroligin-1	protein-containing complex binding binding protein binding signaling receptor binding neurexin family protein binding identical protein binding molecular transducer activity signaling receptor activity PDZ domain binding protein domain specific binding cell adhesion molecule binding scaffold protein binding	developmental process multicellular organismal process nervous system development developmental maturation synapse maturation cellular component organization cell-cell adhesion involved in synapse maturation multicellular organism development cell adhesion cell junction organization cell-cell adhesion anatomical structure development cellular process synapse organization developmental process multicellular organismal process nervous system development developmental maturation synapse maturation cellular component organization cell-cell adhesion involved in synapse maturation multicellular organism development cell adhesion cell junction organization cell-cell adhesion anatomical structure development cellular process synapse organization cellular component organization or biogenesis system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling membrane organization cellular localization postsynapse organization AMPA glutamate receptor clustering glutamate receptor clustering neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane localization receptor clustering macromolecule localization intracellular protein localization postsynaptic membrane organization vesicle localization establishment of organelle localization transport establishment of vesicle localization establishment of localization organelle localization establishment of localization in cell synaptic vesicle localization synaptic vesicle transport membrane biogenesis presynaptic membrane assembly cellular component biogenesis presynaptic membrane organization cellular component assembly cell junction assembly presynapse organization membrane assembly neurexin clustering involved in presynaptic membrane assembly synapse assembly presynapse assembly heterophilic cell-cell adhesion organelle organization postsynaptic density protein 95 clustering postsynaptic density organization postsynaptic specialization organization regulation of developmental process cellular developmental process cell projection organization positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development positive regulation of developmental process neurogenesis neuron differentiation dendrite development cell differentiation dendritic spine development plasma membrane bounded cell projection organization generation of neurons neuron development maintenance of synapse structure cell junction maintenance cellular component maintenance cellular response to metal ion cellular response to chemical stimulus response to metal ion response to chemical cellular response to calcium ion response to calcium ion positive regulation of neuromuscular synaptic transmission regulation of neuromuscular synaptic transmission positive regulation of synaptic transmission neuromuscular synaptic transmission regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization regulation of cell projection organization regulation of plasma membrane bounded cell projection organization neuron cell-cell adhesion regulation of postsynaptic specialization assembly regulation of excitatory synapse assembly regulation of synapse structure or activity regulation of synapse assembly regulation of postsynaptic density organization organelle assembly postsynaptic specialization assembly postsynapse assembly regulation of postsynapse organization regulation of cellular component biogenesis regulation of organelle organization excitatory synapse assembly regulation of cell junction assembly regulation of synapse organization regulation of organelle assembly postsynaptic density assembly regulation of postsynaptic density assembly positive regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction establishment of protein localization protein targeting regulation of localization regulated exocytosis positive regulation of neurotransmitter secretion synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport vesicle-mediated transport in synapse positive regulation of regulated secretory pathway positive regulation of neurotransmitter transport neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport regulation of secretion signal release from synapse exocytosis positive regulation of secretion by cell positive regulation of exocytosis regulation of regulated secretory pathway regulation of secretion by cell secretion by cell positive regulation of secretion signal release positive regulation of synaptic vesicle exocytosis regulation of transport secretion regulation of neurotransmitter transport export from cell regulation of vesicle-mediated transport positive regulation of transport regulation of neurotransmitter secretion regulation of exocytosis cortical cytoskeleton organization cytoskeleton organization cytoskeletal matrix organization at active zone ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway NMDA selective glutamate receptor signaling pathway NMDA glutamate receptor clustering presynaptic active zone organization positive regulation of presynaptic active zone assembly regulation of presynapse assembly regulation of presynaptic active zone assembly regulation of presynapse organization positive regulation of presynapse assembly presynaptic active zone assembly calcium-dependent cell-cell adhesion ruffle organization plasma membrane bounded cell projection assembly ruffle assembly positive regulation of cellular component biogenesis regulation of cell projection assembly positive regulation of ruffle assembly regulation of plasma membrane bounded cell projection assembly regulation of ruffle assembly cell projection assembly positive regulation of plasma membrane bounded cell projection assembly terminal button organization protein localization to synapse regulation of protein localization positive regulation of protein localization to synapse regulation of protein localization to synapse positive regulation of protein localization protein localization to cell junction positive regulation of nervous system development regulation of nervous system development regulation of multicellular organismal development positive regulation of cell junction assembly positive regulation of multicellular organismal process positive regulation of synapse assembly synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission, glutamatergic regulation of signaling receptor activity regulation of transmembrane transporter activity regulation of NMDA receptor activity transmembrane transport regulation of molecular function regulation of transmembrane transport regulation of neurotransmitter receptor activity synaptic membrane adhesion positive regulation of synaptic transmission, GABAergic synaptic transmission, GABAergic regulation of synaptic transmission, GABAergic respiratory gaseous exchange by respiratory system respiratory system process regulation of respiratory gaseous exchange regulation of respiratory system process regulation of respiratory gaseous exchange by nervous system process receptor localization to synapse synaptic vesicle clustering positive regulation of synaptic vesicle clustering regulation of synaptic vesicle clustering plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis anatomical structure morphogenesis neuronal ion channel clustering anatomical structure maturation neuron maturation cell maturation negative regulation of biological process negative regulation of dendritic spine morphogenesis dendritic spine morphogenesis dendritic spine organization negative regulation of cellular component organization negative regulation of dendritic spine development negative regulation of cellular process negative regulation of cell projection organization regulation of anatomical structure morphogenesis negative regulation of developmental process dendrite morphogenesis cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development regulation of dendritic spine morphogenesis neuron projection organization regulation of cell differentiation regulation of neuron differentiation rhythmic process AMPA selective glutamate receptor signaling pathway filopodium assembly regulation of filopodium assembly positive regulation of filopodium assembly postsynaptic membrane assembly neuron projection arborization circadian sleep/wake cycle rhythmic behavior circadian rhythm regulation of circadian sleep/wake cycle regulation of circadian sleep/wake cycle, wakefulness regulation of circadian rhythm behavior regulation of behavior circadian behavior positive regulation of behavior positive regulation of circadian rhythm circadian sleep/wake cycle, wakefulness positive regulation of circadian sleep/wake cycle, wakefulness circadian sleep/wake cycle process synaptic vesicle targeting vesicle targeting exocytic process long-term synaptic potentiation regulation of synaptic plasticity import into cell positive regulation of synaptic vesicle recycling regulation of synaptic vesicle recycling presynaptic endocytosis synaptic vesicle recycling positive regulation of endocytosis regulation of synaptic vesicle endocytosis positive regulation of synaptic vesicle endocytosis regulation of endocytosis synaptic vesicle endocytosis endocytosis	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein complex involved in cell-cell adhesion protein-containing complex protein complex involved in cell adhesion synaptic cleft extracellular region somatodendritic compartment cell projection cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein complex involved in cell-cell adhesion protein-containing complex protein complex involved in cell adhesion synaptic cleft extracellular region somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse cell junction glutamatergic synapse receptor complex neuromuscular junction membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system dendritic shaft neuron spine dendritic spine postsynapse neuron to neuron synapse inhibitory synapse filopodium tip actin-based cell projection filopodium postsynaptic specialization membrane postsynaptic specialization synaptic membrane postsynaptic membrane plasma membrane region presynapse GABA-ergic synapse excitatory synapse postsynaptic density asymmetric synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR050372	Neurexin-related cell adhesion and synaptic protein	Family
E, F, G, H	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
E, F, G, H	IPR000742	EGF-like domain	Domain
E, F, G, H	IPR001791	Laminin G domain	Domain
E, F, G, H	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
E, F, G, H	IPR003585	Neurexin/syndecan/glycophorin C	Domain
A, B, C, D	IPR051093	Neuroligin and Bile salt-activated lipase	Family
A, B, C, D	IPR002018	Carboxylesterase, type B	Domain
A, B, C, D	IPR019819	Carboxylesterase type B, conserved site	Conserved Site
A, B, C, D	IPR000460	Neuroligin	Family
A, B, C, D	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F, G, H	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	Alpha/beta-hydrolases	Acetylcholinesterase-like

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.