5E0Q

Crystal structure of the Nup98 C-terminal domain bound to nanobody TP377

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)
A	d5e0qa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Nup98 autoproteolytic domain-like	8097989	4007737	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	ZU5 domain-like	8097990	3002026	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)
A	PF07686	e5e0qA1	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)
B	PF04096	e5e0qB1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: ZU5/Nup98-C/GAIN-B autoproteolytic domain-related (From Topology)	T: ZU5/Nup98-C/GAIN-B autoproteolytic domain-related	F: PF04096	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.30.1610.10	Alpha Beta	2-Layer Sandwich	c-terminal autoproteolytic domain of nucleoporin nup98	Peptidase S59, nucleoporin	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
A	Nanobody TP377, anti-Nup98	VH	Vicugna pacos (alpaca)	IGHV3S7201, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202417-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Heavy Chain	IGHV1	-	nuclear pore complex protein nup98-nup96	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF04096	Nucleoporin autopeptidase (Nucleoporin2)	Nucleoporin autopeptidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Anti-Nup98 Nanobody TP377	-	-	-
B	Nuclear pore complex protein Nup98-Nup96	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	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 nuclear membrane 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 nuclear membrane membrane organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR036903	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily	Homologous Superfamily
B	IPR025574	Nucleoporin FG repeat	Repeat
B	IPR007230	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain	Domain
B	IPR037665	Nucleoporin peptidase S59-like	Family
B	IPR021967	Nuclear pore complex protein NUP96, C-terminal domain	Domain

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 R01GM133198.