5CWS | pdb_00005cws

Crystal structure of the intact Chaetomium thermophilum Nsp1-Nup49-Nup57 channel nucleoporin heterotrimer bound to its Nic96 nuclear pore complex attachment site

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2 Family	Nup54-like	8049315	4006450	SCOP2 (2022-06-29)
K	SCOP2 Superfamily	Nup54-like	8053270	3002171	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	Nup54-like	8053270	3002171	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Nup62-like	8053266	3002170	SCOP2B (2022-06-29)
C	SCOP2 Family	Nup62-like	8046767	4005288	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Nup62-like	8053266	3002170	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
K	EUF08788	e5cwsK1	A: extended segments	X: Nup54 C-terminal interacting domain (From Topology)	H: Nup54 C-terminal interacting domain (From Topology)	T: Nup54 C-terminal interacting domain	F: EUF08788	ECOD (1.6)
E	EUF08788	e5cwsE1	A: extended segments	X: Nup54 C-terminal interacting domain (From Topology)	H: Nup54 C-terminal interacting domain (From Topology)	T: Nup54 C-terminal interacting domain	F: EUF08788	ECOD (1.6)
J	EUF08166	e5cwsJ1	A: alpha bundles	X: Nucleoporin p58/p45 helical region (From Topology)	H: Nucleoporin p58/p45 helical region (From Topology)	T: Nucleoporin p58/p45 helical region	F: EUF08166	ECOD (1.6)
H	V-set_8	e5cwsH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
H	C1-set_1	e5cwsH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B	V-set_8	e5cwsB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	C1-set_1	e5cwsB3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
G	C1-set_4	e5cwsG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
G	V-set	e5cwsG2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
A	C1-set_4	e5cwsA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A	V-set	e5cwsA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, H	sAB-158 Fab	VH-CH1	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202540-0)
A, G	sAB-158 Fab	L-KAPPA	Homo sapiens (human)	IGKV1D-1301, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202540-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, H	Heavy Chain	IGHV3	-	nucleoporin nup57 \| nucleoporin nsp1 \| nucleoporin nup49 \| nucleoporin nic96	SAbDab (2025-10-17)
A, G	Light Chain	IGKV1	Kappa	nucleoporin nup57 \| nucleoporin nsp1 \| nucleoporin nup49 \| nucleoporin nic96	SAbDab (2025-10-17)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, K	PF18570	NUP57/Nup54 C-terminal domain (Nup54_57_C)	NUP57/Nup54 C-terminal domain	-	Coiled-coil
E, K	PF13874	Nucleoporin complex subunit 54 (Nup54)	Nucleoporin complex subunit 54	-	Coiled-coil
D, J	PF21121	Nucleoporin Nup49 C-terminal helical region (Nup49_C)	Nucleoporin Nup49 C-terminal helical region	-	Family
C, I	PF05064	Nsp1-like C-terminal region (Nsp1_C)	Nsp1-like C-terminal region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F, L	Nucleoporin NIC96	structural molecule activity structural constituent of nuclear pore	cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport localization mRNA export from nucleus establishment of localization in cell RNA localization nuclear export nucleobase-containing compound transport RNA transport nucleic acid transport poly(A)+ mRNA export from nucleus intracellular transport gene expression establishment of localization macromolecule biosynthetic process RNA export from nucleus establishment of RNA localization biosynthetic process macromolecule localization cellular process metabolic process macromolecule metabolic process establishment of protein localization protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane organelle membrane
E, K	Nucleoporin NUP57	structural molecule activity structural constituent of nuclear pore	cellular component organization nucleus organization organelle organization nuclear pore organization protein-containing complex organization cellular process cellular component organization or biogenesis cellular localization protein localization to nucleus localization within membrane protein localization to membrane protein localization to nuclear envelope localization protein localization to organelle cellular component organization nucleus organization organelle organization nuclear pore organization protein-containing complex organization cellular process cellular component organization or biogenesis cellular localization protein localization to nucleus localization within membrane protein localization to membrane protein localization to nuclear envelope localization protein localization to organelle macromolecule localization intracellular protein localization protein localization to nuclear inner membrane establishment of protein localization NLS-bearing protein import into nucleus nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport establishment of localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell protein import into nucleus intracellular protein transport RNA transport nucleic acid transport mRNA transport establishment of RNA localization RNA localization nucleobase-containing compound transport	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 protein-containing complex 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 protein-containing complex nuclear protein-containing complex nuclear pore nuclear pore central transport channel
D, J	Nucleoporin NUP49	structural molecule activity structural constituent of nuclear pore nuclear localization sequence binding signal sequence binding binding peptide binding	RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport establishment of protein localization protein transport intracellular protein localization	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope nuclear pore nuclear membrane membrane organelle membrane
C, I	Nucleoporin NSP1	binding phospholipid binding lipid binding structural molecule activity structural constituent of nuclear pore	establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus cellular process intracellular protein localization intracellular protein transport RNA transport nucleic acid transport mRNA transport establishment of RNA localization RNA localization nucleobase-containing compound transport RNA export from nucleus nuclear export	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 protein-containing complex 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 protein-containing complex nuclear protein-containing complex nuclear pore nuclear pore central transport channel
B, H	sAB-158 Fab Heavy Chain	-	-	-
A, G	sAB-158 Fab Light Chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F, L	IPR007231	Nucleoporin interacting component Nup93/Nic96	Family
E, K	IPR025712	Nucleoporin Nup54, alpha-helical domain	Domain
E, K	IPR024864	Nucleoporin Nup54/Nup57/Nup44	Family
D, J	IPR024882	Nucleoporin p58/p45/NUP49	Family
D, J	IPR025574	Nucleoporin FG repeat	Repeat
C, I	IPR007758	Nucleoporin, NSP1-like, C-terminal	Domain
C, I	IPR025574	Nucleoporin FG repeat	Repeat
C, I	IPR026010	Nucleoporin NSP1/NUP62	Family

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.