3NF5 | pdb_00003nf5

Crystal structure of the C-terminal domain of nuclear pore complex component NUP116 from Candida glabrata

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	ZU5 domain-like	8099806	3002026	SCOP2B (2022-06-29)
A	SCOP2 Family	Nup98 autoproteolytic domain-like	8099805	4007737	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ZU5 domain-like	8099806	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)
B	F5_F8_type_C	e3nf5B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: F5_F8_type_C	ECOD (v294.1)
A	OmpA	e3nf5A1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Creatinase/prolidase N-terminal domain	T: Creatinase/prolidase N-terminal domain	F: OmpA	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1610.10	Alpha Beta	2-Layer Sandwich	c-terminal autoproteolytic domain of nucleoporin nup98	Peptidase S59, nucleoporin	CATH (4.3.0)
A	3.30.1610.10	Alpha Beta	2-Layer Sandwich	c-terminal autoproteolytic domain of nucleoporin nup98	Peptidase S59, nucleoporin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04096	Nup98-96 autopeptidase S59 (Nucleoporin2)	Nup98-96 autopeptidase S59	The nuclear pore complex protein plays a role in bidirectional transport across the nucleoporin complex in nucleocytoplasmic transport. The mammalian nuclear pore complex (NPC) is comprised of approximately 30 unique proteins, collectively known as n ...	The nuclear pore complex protein plays a role in bidirectional transport across the nucleoporin complex in nucleocytoplasmic transport. The mammalian nuclear pore complex (NPC) is comprised of approximately 30 unique proteins, collectively known as nucleoporins [2]. This entry includes yeast family members such as Nup145p as well as vertebrate Nup98. The NUP C-terminal domains of Nup98 and Nup145 possess peptidase S59 autoproteolytic activity. The autoproteolytic sites of Nup98 and Nup145 each occur immediately C-terminal to the NUP C-terminal domain. Thus, although this domain occurs in the middle of each precursor polypeptide, it winds up at the C-terminal end of the N-terminal cleavage product. Cleavage of the peptide chains are necessary for the proper targeting to the nuclear pore [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Nucleoporin NUP116	RNA binding binding nucleic acid binding structural molecule activity structural constituent of nuclear pore ATPase binding protein binding enzyme binding identical protein binding nuclear localization sequence binding signal sequence binding peptide binding	cellular component organization nucleus organization organelle organization nuclear pore organization protein-containing complex organization cellular process cellular component organization or biogenesis localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization cellular localization nitrogen compound transport cellular component organization nucleus organization organelle organization nuclear pore organization protein-containing complex organization cellular process cellular component organization or biogenesis localization telomere localization telomere tethering at nuclear periphery chromosome localization organelle localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport mRNA transport 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 metabolic process macromolecule metabolic process tRNA export from nucleus tRNA transport chromosome organization transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery establishment of organelle localization ribonucleoprotein complex biogenesis ribosomal subunit export from nucleus ribosomal large subunit export from nucleus cellular component biogenesis ribosome biogenesis ribosome localization 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 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 nuclear pore cytoplasmic filaments

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR025574	Nucleoporin FG repeat	Repeat
A, B	IPR037665	Nucleoporin peptidase S59-like	Family
A, B	IPR036903	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily	Homologous Superfamily
A, B	IPR007230	Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.