4BSZ | pdb_00004bsz

Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1

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	SCOP2 Family	Ankyrin repeat	8088392	4000366	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ankyrin repeat	8088393	3000154	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	Tubulin	e4bszB1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Tubulin	ECOD (v294.1)
A	Tubulin	e4bszA1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F: Tubulin	ECOD (v294.1)
A	HTH_24	e4bszA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: HTH_24	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
A	3.30.300.20	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat
A	PF07650	KH domain (KH_2)	KH domain		Domain
A	PF00189	Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)	Ribosomal protein S3, C-terminal domain	This family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	ANKYRIN REPEAT-CONTAINING PROTEIN YAR1	unfolded protein binding protein binding binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization cellular component biogenesis localization ribosome biogenesis intercellular transport ribosomal small subunit export from nucleus organelle localization establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization cellular component biogenesis localization ribosome biogenesis intercellular transport ribosomal small subunit export from nucleus organelle localization establishment of localization in cell cellular process cellular component organization or biogenesis nuclear export ribosome localization regulation of localization regulation of biological process regulation of protein localization macromolecule localization biological regulation intracellular protein localization ribosomal small subunit biogenesis regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process response to osmotic stress response to stimulus response to stress response to abiotic stimulus cellular response to stimulus response to oxidative stress cellular response to chemical stimulus cellular response to stress response to chemical cellular response to oxidative stress cellular response to chemical stress	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle intracellular organelle MBF transcription complex cellular anatomical structure organelle cytoplasm SBF transcription complex
A	40S RIBOSOMAL PROTEIN S3	DNA-(apurinic or apyrimidinic site) endonuclease activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity RNA binding binding nucleic acid binding structural molecule activity structural constituent of ribosome	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process establishment of organelle localization cellular localization ribonucleoprotein complex biogenesis nucleocytoplasmic transport transport nuclear transport ribosomal subunit export from nucleus intracellular transport establishment of localization cellular component biogenesis localization ribosome biogenesis intercellular transport ribosomal small subunit export from nucleus organelle localization establishment of localization in cell cellular component organization or biogenesis nuclear export ribosome localization nonfunctional rRNA decay catabolic process RNA metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process maintenance of translational fidelity	preribosome protein-containing complex ribonucleoprotein complex preribosome, small subunit precursor cellular anatomical structure intracellular anatomical structure cytoplasm cytosol 90S preribosome cytosolic small ribosomal subunit small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit preribosome protein-containing complex ribonucleoprotein complex preribosome, small subunit precursor cellular anatomical structure intracellular anatomical structure cytoplasm cytosol 90S preribosome cytosolic small ribosomal subunit small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle membraneless organelle ribosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR002110	Ankyrin repeat	Repeat
B	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR005703	Small ribosomal subunit protein uS3, eukaryota/archaeal	Family
A	IPR001351	Small ribosomal subunit protein uS3, C-terminal	Domain
A	IPR057258	Small ribosomal subunit protein uS3	Family
A	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
A	IPR004044	K Homology domain, type 2	Domain
A	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
A	IPR036419	Ribosomal protein S3, C-terminal domain superfamily	Homologous Superfamily
A	IPR018280	Small ribosomal subunit protein uS3, conserved site	Conserved Site

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.