3LYV | pdb_00003lyv

Crystal structure of a domain of ribosome-associated factor Y from streptococcus pyogenes serotype M6. Northeast Structural Genomics Consortium target id DR64A

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)
D	SCOP2 Family	Hibernation promoting factor (HPF), C-terminal domain-like	8045351	4004430	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Hibernation promoting factor (HPF), C-terminal domain-like	8052700	3002136	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Hibernation promoting factor (HPF), C-terminal domain-like	8052700	3002136	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Hibernation promoting factor (HPF), C-terminal domain-like	8052700	3002136	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Hibernation promoting factor (HPF), C-terminal domain-like	8052700	3002136	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)
F	Ribosom_S30AE_C	e3lyvF1	A: a+b two layers	X: Ribosome-associated factor Y (From Topology)	H: Ribosome-associated factor Y (From Topology)	T: Ribosome-associated factor Y	F: Ribosom_S30AE_C	ECOD (1.6)
E	Ribosom_S30AE_C	e3lyvE1	A: a+b two layers	X: Ribosome-associated factor Y (From Topology)	H: Ribosome-associated factor Y (From Topology)	T: Ribosome-associated factor Y	F: Ribosom_S30AE_C	ECOD (1.6)
D	Ribosom_S30AE_C	e3lyvD1	A: a+b two layers	X: Ribosome-associated factor Y (From Topology)	H: Ribosome-associated factor Y (From Topology)	T: Ribosome-associated factor Y	F: Ribosom_S30AE_C	ECOD (1.6)
C	Ribosom_S30AE_C	e3lyvC1	A: a+b two layers	X: Ribosome-associated factor Y (From Topology)	H: Ribosome-associated factor Y (From Topology)	T: Ribosome-associated factor Y	F: Ribosom_S30AE_C	ECOD (1.6)
B	Ribosom_S30AE_C	e3lyvB1	A: a+b two layers	X: Ribosome-associated factor Y (From Topology)	H: Ribosome-associated factor Y (From Topology)	T: Ribosome-associated factor Y	F: Ribosom_S30AE_C	ECOD (1.6)
A	Ribosom_S30AE_C	e3lyvA1	A: a+b two layers	X: Ribosome-associated factor Y (From Topology)	H: Ribosome-associated factor Y (From Topology)	T: Ribosome-associated factor Y	F: Ribosom_S30AE_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.505.50	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain	CATH (4.2.0)
E	3.30.505.50	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain	CATH (4.2.0)
D	3.30.505.50	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain	CATH (4.2.0)
C	3.30.505.50	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain	CATH (4.2.0)
B	3.30.505.50	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain	CATH (4.2.0)
A	3.30.505.50	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF16321	Sigma 54 modulation/S30EA ribosomal protein C terminus (Ribosom_S30AE_C)	Sigma 54 modulation/S30EA ribosomal protein C terminus	This domain often occurs at the C-terminus of proteins containing Pfam:PF02482.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Ribosome-associated factor Y	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, E A, B, C, D, E, F	IPR003489	Ribosome hibernation promoting factor/RaiA	Family
A, B, C, D, E A, B, C, D, E, F	IPR034694	Ribosome hibernation promoting factor, long/plastid	Family
A, B, C, D, E A, B, C, D, E, F	IPR036567	Ribosome hibernation promotion factor-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR032528	Sigma 54 modulation/S30EA ribosomal protein, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038416	Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	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.