5C3L | pdb_00005c3l

Structure of the metazoan Nup62.Nup58.Nup54 nucleoporin complex.

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5c3ld1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	Arabian camel (Camelus dromedarius ) [TaxId: 9838 ],	SCOPe (2.08)
D	d5c3ld2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Arabian camel (Camelus dromedarius ) [TaxId: 9838 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Nup58-like	8044823	4004156	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Nup58-like	8053258	3002169	SCOP2 (2022-06-29)
C	SCOP2 Family	Nup62-like	8046765	4005288	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Nup62-like	8053261	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)
D	V-set_8	e5c3lD1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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
D	Nanobody Nb15	VH	Camelus dromedarius (Arabian camel)	IGHV3S2701, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202543-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D	Heavy Chain	IGHV3	-	nucleoporin nup62 \| nup54 \| nucleoporin nup58	SAbDab (2025-11-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13874	Nucleoporin complex subunit 54 (Nup54)	Nucleoporin complex subunit 54	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Nucleoporin Nup58	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
D	Nanobody Nb15	-	-	-
E [auth H]	Part of Nup54 N-terminus with weak electron density, built as poly-alanine.	-	-	-
C	Nucleoporin Nup62	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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle nuclear membrane cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system organelle envelope nuclear envelope organelle membrane protein-containing complex nuclear protein-containing complex nuclear pore nuclear pore central transport channel centrosome microtubule organizing center
A	Nup54	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR024882	Nucleoporin p58/p45/NUP49	Family
C	IPR007758	Nucleoporin, NSP1-like, C-terminal	Domain
C	IPR026010	Nucleoporin NSP1/NUP62	Family
A	IPR025712	Nucleoporin Nup54, alpha-helical domain	Domain
A	IPR040985	Nup54, C-terminal interacting domain	Domain
A	IPR024864	Nucleoporin Nup54/Nup57/Nup44	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.