5C3L

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	PF07686	e5c3lD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	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 (202416-0)

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 (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF13874	Nucleoporin complex subunit 54 (Nup54)	Nucleoporin complex subunit 54	This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and ...	This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them [1,2].	Domain
B	PF15967	Nucleoporin FG repeated region (Nucleoporin_FG2)	Nucleoporin FG repeated region	-	Family
C	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
A	Nup54	-	-	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope nuclear pore
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 organic substance transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport protein localization establishment of protein localization RNA transport nitrogen compound transport transport organic substance transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport protein localization establishment of protein localization cellular localization protein transport cellular macromolecule localization cellular process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope nuclear pore
C	Nucleoporin Nup62	structural molecule activity structural constituent of nuclear pore	RNA transport nitrogen compound transport transport organic substance transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport protein localization establishment of protein localization RNA transport nitrogen compound transport transport organic substance transport nucleic acid transport mRNA transport establishment of localization localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport protein localization establishment of protein localization cellular localization protein transport cellular macromolecule localization cellular process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle protein-containing complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope nuclear pore
D	Nanobody Nb15	-	-	-
E [auth H]	Part of Nup54 N-terminus with weak electron density, built as poly-alanine.	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.