2YWQ | pdb_00002ywq

Crystal structure of Thermus thermophilus Protein Y N-terminal domain

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2ywqb_	Alpha and beta proteins (a+b)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2ywqc_	Alpha and beta proteins (a+b)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D	d2ywqd_	Alpha and beta proteins (a+b)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2ywqa1	Alpha and beta proteins (a+b)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	Ribosome binding protein Y (YfiA homologue)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	YfiA/CsgE-like	8037928	3000912	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	YfiA/CsgE-like	8037928	3000912	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YfiA/CsgE-like	8037928	3000912	SCOP2B (2022-06-29)
A	SCOP2 Family	YfiA-like	8025549	4003461	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YfiA/CsgE-like	8037928	3000912	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	RF-1	e2ywqB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RF-1	ECOD (v294.1)
C	RF-1	e2ywqC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RF-1	ECOD (v294.1)
D	RF-1	e2ywqD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RF-1	ECOD (v294.1)
A	Ribosomal_S30AE	e2ywqA1	A: a+b two layers	X: dsRBD-like	H: Ribosome binding protein Y (YfiA homologue)	T: Ribosome binding protein Y (YfiA homologue)	F: Ribosomal_S30AE	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.160.100	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Ribosome hibernation promotion factor-like	CATH (4.3.0)
C	3.30.160.100	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Ribosome hibernation promotion factor-like	CATH (4.3.0)
D	3.30.160.100	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Ribosome hibernation promotion factor-like	CATH (4.3.0)
A	3.30.160.100	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Ribosome hibernation promotion factor-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02482	Sigma 54 modulation protein / S30EA ribosomal protein (Ribosomal_S30AE)	Sigma 54 modulation protein / S30EA ribosomal protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Ribosomal subunit interface protein	ribonucleoprotein complex binding protein-containing complex binding binding ribosomal small subunit binding ribosome binding	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translational elongation negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process negative regulation of translational elongation regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003489	Ribosome hibernation promoting factor/RaiA	Family
A, B, C, D	IPR034694	Ribosome hibernation promoting factor, long/plastid	Family
A, B, C, D	IPR036567	Ribosome hibernation promotion factor-like	Homologous Superfamily
A, B, C, D	IPR032528	Sigma 54 modulation/S30EA ribosomal protein, C-terminal	Domain
A, B, C, D	IPR038416	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR050574	HPF/YfiA ribosome-associated	Family

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.