5U4J

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
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)
H [auth l]	SCOP2B Superfamily	Nucleic acid-binding proteins	8106545	3000135	SCOP2B (2022-06-29)
I [auth v]	SCOP2B Superfamily	RNA-binding domain RBD	8054399	3000110	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)
E [auth e]	PF03719	e5u4je2	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: PF03719	ECOD (1.6)
E [auth e]	PF00333	e5u4je1	A: a+b two layers	X: dsRBD-like	H: dsRNA-binding domain-like (From Topology)	T: dsRNA-binding domain-like	F: PF00333	ECOD (1.6)
H [auth l]	PF00164	e5u4jl1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF00164	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
H [auth l]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth c]	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
D [auth d]	PF00163	Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)	Ribosomal protein S4/S9 N-terminal domain	-	Family
J [auth w]	PF03889	Alternative ribosome-rescue factor A (ArfA)	Alternative ribosome-rescue factor A	During translation of messenger RNAs by ribosomes, translation sometimes pauses or stalls. Ribosomes stalled on mRNAs need to be rescued for reuse in order to maintain proper translation capacity. Rescue systems such as ArfA-RF2 and ArfB (formerly kn ...	During translation of messenger RNAs by ribosomes, translation sometimes pauses or stalls. Ribosomes stalled on mRNAs need to be rescued for reuse in order to maintain proper translation capacity. Rescue systems such as ArfA-RF2 and ArfB (formerly known as YaeJ) are present in many bacterial species. Family members such as ArfA cooperates with the canonical peptide release factor RF2 to hydrolyse the peptidyl-tRNA in the non-stop complex. Structural and biochemical analysis show that ArfA anchors its positively charged C-terminal in the mRNA entry channel of the ribosome. Whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2 thereby triggering RF2 peptidyl-hydrolysing activity [1] [2].	Domain
E [auth e]	PF03719	Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)	Ribosomal protein S5, C-terminal domain	-	Domain
E [auth e]	PF00333	Ribosomal protein S5, N-terminal domain (Ribosomal_S5)	Ribosomal protein S5, N-terminal domain	-	Domain
H [auth l]	PF00164	Ribosomal protein S12/S23 (Ribosom_S12_S23)	Ribosomal protein S12/S23	-	Family
I [auth v]	PF03462	PCRF domain (PCRF)	PCRF domain	This domain is found in peptide chain release factors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth c]	30S ribosomal protein S3	RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding rRNA binding structural molecule activity structural constituent of ribosome	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cytoplasmic translation metabolic process cellular process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization non-membrane-bounded 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle
D [auth d]	30S ribosomal protein S4	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding mRNA 5'-UTR binding mRNA binding translation regulator activity mRNA regulatory element binding translation repressor activity translation regulator activity, nucleic acid binding 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 negative regulation of cellular metabolic process 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 organic substance biosynthetic 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 negative regulation of cellular metabolic process 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 organic substance biosynthetic 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 cellular metabolic process negative regulation of metabolic process regulation of cellular metabolic process primary metabolic process negative regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound 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 cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process DNA-templated transcription termination RNA biosynthetic process cellular component organization nucleic acid biosynthetic process organic substance metabolic 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 regulation of cellular biosynthetic process positive regulation of gene expression negative regulation of biosynthetic process cellular process positive regulation of cellular biosynthetic process organonitrogen compound metabolic process organonitrogen compound biosynthetic process translation 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 non-membrane-bounded 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 cellular anatomical entity ribosomal subunit intracellular organelle organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit cellular anatomical entity ribosomal subunit intracellular organelle organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle cytoplasm cytosol cytosolic small ribosomal subunit cytosolic ribosome
A [auth a]	16S 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 organic cyclic compound binding tRNA binding nucleic acid binding rRNA binding	regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process rescue of stalled ribosome cellular component organization organelle disassembly cellular component organization or biogenesis cellular component disassembly ribosome disassembly organelle organization translational elongation	-
B [auth A]	23S rRNA	-	-	-
E [auth e]	30S ribosomal protein S5	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cytoplasmic translation metabolic process cellular process organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance 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 non-membrane-bounded 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle
F [auth z]	mRNA	-	-	-
G [auth x]	P-site tRNA fMet	-	-	-
H [auth l]	30S ribosomal protein S12	RNA binding binding organic cyclic compound binding rRNA binding nucleic acid binding misfolded RNA binding tRNA binding structural molecule activity structural constituent of ribosome	regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of cellular process cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process RNA processing regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biosynthetic process RNA splicing positive regulation of nucleobase-containing compound metabolic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression regulation of RNA splicing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of cellular biosynthetic process organic cyclic compound 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 positive regulation of cellular biosynthetic process organonitrogen compound metabolic process organonitrogen compound biosynthetic process translation 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	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome non-membrane-bounded organelle
I [auth v]	Peptide chain release factor 2	translation release factor activity, codon specific translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation release factor activity nucleic acid binding translation termination factor activity translation factor activity, RNA binding	cellular component disassembly organonitrogen compound metabolic process protein-containing complex organization cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process protein-containing complex disassembly primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization organic substance metabolic process biosynthetic process organic substance biosynthetic process cellular component disassembly organonitrogen compound metabolic process protein-containing complex organization cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process protein-containing complex disassembly primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization organic substance metabolic process biosynthetic process organic substance biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis protein metabolic process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth c]	IPR001351	Small ribosomal subunit protein uS3, C-terminal	Domain
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]	IPR005704	Small ribosomal subunit protein uS3, bacterial-type	Family
C [auth c]	IPR018280	Small ribosomal subunit protein uS3, conserved site	Conserved Site
D [auth d]	IPR002942	RNA-binding S4 domain	Domain
D [auth d]	IPR005709	Small ribosomal subunit protein uS4, bacterial-type	Family
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
J [auth w]	IPR005589	Alternative ribosome-rescue factor A	Family
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]	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]	IPR005712	Small ribosomal subunit protein uS5, bacterial-type	Family
E [auth e]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
H [auth l]	IPR005679	Ribosomal protein uS12, bacterial-type	Family
H [auth l]	IPR006032	Small ribosomal subunit protein uS12	Family
H [auth l]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
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