1T5Y | pdb_00001t5y

Crystal Structure of Northeast Structural Genomics Consortium Target HR2118: A Human Homolog of Saccharomyces cerevisiae Nip7p

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1t5ya1	All beta proteins	PUA domain-like	PUA domain-like	PUA domain	Nip7p homolog, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1t5ya2	Alpha and beta proteins (a+b)	Cystatin-like	Pre-PUA domain	Nip7p homolog, N-terminal domain	Nip7p homolog, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PUA domain-like	8032383	3001015	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pre-PUA domain	8032388	3001126	SCOP2B (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	PUA	e1t5yA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: PUA	ECOD (1.6)
A	KOG3492	e1t5yA2	A: a+b two layers	X: Cystatin-like	H: Pre-PUA domain (From Topology)	T: Pre-PUA domain	F: KOG3492	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.450.220	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	2.30.130.10	Mainly Beta	Roll	Archaeosine Trna-guanine Transglycosylase	Chain: A, domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03657	UPF0113 PUA domain (UPF0113)	UPF0113 PUA domain		Domain
A	PF17833	NIP7/UPF0113, pre-PUA domain (pre-PUA_NIP7)	NIP7/UPF0113, pre-PUA domain	This entry represents the N-terminal, pre-PUA domain of yeast 60S ribosome subunit biogenesis protein NIP7 and homologues, some uncharacterised proteins from the UPF0113 family and similar sequences from eukaryotes and some archaeal species. NIP7 is ...	This entry represents the N-terminal, pre-PUA domain of yeast 60S ribosome subunit biogenesis protein NIP7 and homologues, some uncharacterised proteins from the UPF0113 family and similar sequences from eukaryotes and some archaeal species. NIP7 is required for proper 27S pre-rRNA processing and 60S ribosome subunit assembly. This domain is found associated with Pfam:PF03657.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	SACCHAROMYCES CEREVISIAE Nip7p HOMOLOG	RNA binding binding nucleic acid binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis ribosomal large subunit biogenesis organelle assembly membraneless organelle assembly cellular component organization organelle organization cellular component assembly ribosome assembly	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen preribosome protein-containing complex ribonucleoprotein complex preribosome, large subunit precursor cytoplasm cytosol nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015947	PUA-like superfamily	Homologous Superfamily
A	IPR005155	UPF0113, PUA domain	Domain
A	IPR016686	Ribosome biogenesis factor, NIP7	Family
A	IPR036974	PUA domain superfamily	Homologous Superfamily
A	IPR040598	60S ribosome subunit biogenesis protein NIP7, pre-PUA domain	Domain
A	IPR002478	PUA domain	Domain
A	IPR055359	60S ribosome subunit biogenesis protein Nip7, pre-PUA domain, eukaryotes	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y221	glioblastoma malignant glioma ovarian cancer large cell medulloblastoma Malignant neoplasm of breast lung cancer medulloblastoma

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.