3KQ4 | pdb_00003kq4

Structure of Intrinsic Factor-Cobalamin bound to its receptor Cubilin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)
C	SCOP2 Family	Transcobalamin N-terminal domain-like	8048589	4006152	SCOP2 (2022-06-29)
C	SCOP2 Family	Transcobalamin C-terminal domain-like	8050039	4006739	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	CMD	e3kq4B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: sensor domains	T: sensor domains	F: CMD	ECOD (v294.1)
B	Ribosomal_L24e	e3kq4B3	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Ribosomal_L24e	ECOD (v294.1)
D	Tautomerase_3	e3kq4D1	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Tautomerase/MIF	F: Tautomerase_3	ECOD (v294.1)
D	Ribosomal_L24e	e3kq4D3	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Ribosomal_L24e	ECOD (v294.1)
F	Tautomerase_3	e3kq4F1	A: a/b three-layered sandwiches	X: Tautomerase/MIF-like	H: Tautomerase/MIF	T: Tautomerase/MIF	F: Tautomerase_3	ECOD (v294.1)
F	Ribosomal_L24e	e3kq4F3	A: a/b three-layered sandwiches	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain	T: ssDNA-binding transcriptional regulator domain	F: Ribosomal_L24e	ECOD (v294.1)
A	PaaX	e3kq4A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: HTH	T: winged helix domain	F: PaaX	ECOD (v294.1)
C	RVP	e3kq4C2	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
C	Cobalamin_bind	e3kq4C3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)
E	RVP	e3kq4E2	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (v294.1)
E	Cobalamin_bind	e3kq4E3	A: a/b three-layered sandwiches	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
D	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
F	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
A	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
A	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)
C	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
C	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)
E	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
E	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF00431	CUB domain (CUB)	CUB domain		Domain
A, C, E	PF01122	Eukaryotic cobalamin-binding protein (Cobalamin_bind)	Eukaryotic cobalamin-binding protein	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	Cubilin	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding cargo receptor activity identical protein binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding molecular transducer activity signaling receptor activity vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding cargo receptor activity identical protein binding protein binding protein homodimerization activity protein dimerization activity	secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process lipid metabolic process localization cellular localization establishment of localization in cell establishment of localization secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process alcohol metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process lipid metabolic process localization cellular localization establishment of localization in cell establishment of localization establishment of protein localization protein transport transport macromolecule localization lipoprotein transport intracellular protein localization lipoprotein localization cobalamin metabolic process tetrapyrrole metabolic process nitrogen compound transport vitamin transport cobalamin transport biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus multicellular organismal process multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis import into cell receptor-mediated endocytosis endocytosis vesicle-mediated transport	cellular anatomical structure clathrin-coated pit membrane endomembrane system cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen cellular anatomical structure clathrin-coated pit membrane endomembrane system cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol plasma membrane bounded cell projection cell projection actin-based cell projection microvillus microvillus membrane cell projection membrane intracellular vesicle cytoplasmic vesicle endocytic vesicle protein-containing complex receptor complex vacuolar membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane Golgi apparatus endosome brush border membrane cluster of actin-based cell projections brush border extrinsic component of plasma membrane cell surface extrinsic component of external side of plasma membrane extrinsic component of membrane external side of plasma membrane side of membrane endoplasmic reticulum
A, C, E	Gastric intrinsic factor	molecular carrier activity protein binding binding cargo receptor ligand activity vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding	localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization monoatomic ion transmembrane transport metal ion transport cobalt ion transport monoatomic cation transmembrane transport transmembrane transport transition metal ion transport monoatomic ion transport cellular process localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization monoatomic ion transmembrane transport metal ion transport cobalt ion transport monoatomic cation transmembrane transport transmembrane transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle extracellular region membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole lysosomal lumen intracellular organelle lumen organelle lumen lysosome cell projection actin-based cell projection microvillus plasma membrane bounded cell projection extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR024731	NELL2-like, EGF domain	Domain
B, D, F	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
B, D, F	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B, D, F	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
B, D, F	IPR000859	CUB domain	Domain
B, D, F	IPR000742	EGF-like domain	Domain
B, D, F	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B, D, F	IPR001881	EGF-like calcium-binding domain	Domain
B, D, F	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A, C, E	IPR002157	Cobalamin (vitamin B12)-binding protein	Family
A, C, E	IPR051588	Eukaryotic Cobalamin Transport	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F	Pharos: O60494	melanoma megaloblastic anemia amphetamine abuse Imerslund-Grasbeck syndrome type 1 colorectal cancer Cytopenia proteinuria congenital anemia Dent disease nephrosclerosis cutaneous melanoma osteosarcoma
A, C, E	Pharos: P27352	congenital intrinsic factor deficiency schizophrenia bipolar disorder Crohn disease Congenital deficiency of intrinsic factor pernicious anemia

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.