5U4J | pdb_00005u4j

Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
I [auth v]	SCOP2B Superfamily	RNA-binding domain, RBD	8054399	3000110	SCOP2B (2022-06-29)
H [auth l]	SCOP2B Superfamily	Nucleic acid-binding proteins	8106545	3000135	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)
H [auth l]	Ras	e5u4jl1	A: a/b three-layered sandwiches	X: Small envelope protein M	H: Small envelope protein M	T: Small envelope protein M	F: Ras	ECOD (v294.1)
E [auth e]	Ras	e5u4je1	A: a/b three-layered sandwiches	X: Small envelope protein M	H: Small envelope protein M	T: Small envelope protein M	F: Ras	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth l]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
E [auth e]	3.30.160.20	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain		CATH (utative)
E [auth e]	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth v]	Peptide chain release factor 2	translation release factor activity, codon specific translation factor activity translation release factor activity translation termination factor activity	viral gene expression viral process viral translational frameshifting viral translation cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization biosynthetic process viral gene expression viral process viral translational frameshifting viral translation cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
H [auth l]	30S ribosomal protein S12	RNA binding binding rRNA binding nucleic acid binding misfolded RNA binding tRNA binding structural molecule activity structural constituent of ribosome	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process RNA splicing regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of RNA splicing regulation of metabolic process translation protein biosynthetic process cytoplasmic translation protein metabolic process RNA folding Group I intron splicing RNA splicing, via transesterification reactions with guanosine as nucleophile RNA splicing, via transesterification reactions response to stimulus response to chemical response to antibiotic maintenance of translational fidelity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome
G [auth x]	P-site tRNA fMet	-	-	-
F [auth z]	mRNA	-	-	-
E [auth e]	30S ribosomal protein S5	RNA binding binding rRNA 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 response to stimulus response to chemical response to antibiotic 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 response to stimulus response to chemical response to antibiotic ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribosome assembly maintenance of translational fidelity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome
D [auth d]	30S ribosomal protein S4	RNA binding binding rRNA binding nucleic acid binding mRNA 5'-UTR binding mRNA binding translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity structural molecule activity structural constituent of ribosome	negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process negative regulation of termination of DNA-templated transcription regulation of cellular process negative regulation of biological process protein-containing complex disassembly positive regulation of macromolecule biosynthetic process regulation of protein-containing complex disassembly regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of macromolecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process cellular component disassembly negative regulation of DNA-templated transcription regulation of biological process negative regulation of cellular component organization negative regulation of metabolic process primary metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of cellular component organization transcription antitermination positive regulation of biological process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process positive regulation of biosynthetic process negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis positive regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process protein-containing complex organization biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process positive regulation of gene expression negative regulation of biosynthetic process cellular process translation protein biosynthetic process cytoplasmic translation protein metabolic process response to stimulus response to chemical response to antibiotic cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis ribosomal small subunit biogenesis post-transcriptional regulation of gene expression negative regulation of translation translational initiation negative regulation of protein metabolic process regulation of translational initiation regulation of protein metabolic process negative regulation of translational initiation negative regulation of gene expression regulation of translation organelle assembly membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribosome assembly maintenance of translational fidelity	protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome cytoplasm cytosol cytosolic small ribosomal subunit cytosolic ribosome
C [auth c]	30S ribosomal protein S3	RNA binding binding nucleic acid binding mRNA binding rRNA 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 ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization 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 ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis ribosome assembly	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome
B [auth A]	23S rRNA	-	-	-
J [auth w]	Alternative ribosome-rescue factor A	ribonucleoprotein complex binding protein-containing complex binding binding ribosomal large subunit binding ribosome binding RNA binding tRNA binding nucleic acid binding rRNA binding	regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process cellular component disassembly ribosome disassembly cellular component organization organelle organization organelle disassembly translational elongation cytoplasmic translation cytoplasmic translational elongation cellular component organization or biogenesis rescue of stalled cytosolic ribosome	-
A [auth a]	16S rRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth v]	IPR004374	Peptide chain release factor 2	Family
I [auth v]	IPR000352	Peptide chain release factor class I	Domain
I [auth v]	IPR045853	Peptide chain release factor class I superfamily	Homologous Superfamily
I [auth v]	IPR005139	Peptide chain release factor	Domain
H [auth l]	IPR005679	Ribosomal protein uS12, bacteria	Family
H [auth l]	IPR006032	Small ribosomal subunit protein uS12	Family
H [auth l]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
E [auth e]	IPR000851	Small ribosomal subunit protein uS5	Family
E [auth e]	IPR005324	Small ribosomal subunit protein uS5, C-terminal	Domain
E [auth e]	IPR005712	Small ribosomal subunit protein uS5, bacteria	Family
E [auth e]	IPR013810	Small ribosomal subunit protein uS5, N-terminal	Domain
E [auth e]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
E [auth e]	IPR018192	Small ribosomal subunit protein uS5, N-terminal, conserved site	Conserved Site
E [auth e]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
D [auth d]	IPR002942	RNA-binding S4 domain	Domain
D [auth d]	IPR022801	Small ribosomal subunit protein uS4	Family
D [auth d]	IPR018079	Small ribosomal subunit protein uS4, conserved site	Conserved Site
D [auth d]	IPR001912	Small ribosomal subunit protein uS4, N-terminal	Domain
D [auth d]	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily
D [auth d]	IPR005709	Small ribosomal subunit protein uS4, bacteria	Family
C [auth c]	IPR005704	Small ribosomal subunit protein uS3, bacteria	Family
C [auth c]	IPR001351	Small ribosomal subunit protein uS3, C-terminal	Domain
C [auth c]	IPR057258	Small ribosomal subunit protein uS3	Family
C [auth c]	IPR009019	K homology domain superfamily, prokaryotic type	Homologous Superfamily
C [auth c]	IPR004087	K Homology domain	Domain
C [auth c]	IPR004044	K Homology domain, type 2	Domain
C [auth c]	IPR015946	K homology domain-like, alpha/beta	Homologous Superfamily
C [auth c]	IPR036419	Ribosomal protein S3, C-terminal domain superfamily	Homologous Superfamily
C [auth c]	IPR018280	Small ribosomal subunit protein uS3, conserved site	Conserved Site
J [auth w]	IPR005589	Alternative ribosome-rescue factor A	Family