5u4j

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

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

30S ribosomal protein S3

OrganismNot specified

UniProt P0A7V3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 16S rRNA × 1 23S rRNA × 1 30S ribosomal protein S4 × 1 (P0A7V8) 30S ribosomal protein S5 × 1 (P0A7W1) mRNA × 1 P-site tRNA fMet × 1 30S ribosomal protein S12 × 1 (P0A7S3) Peptide chain release factor 2 × 1 (P07012) Alternative ribosome-rescue factor A × 1 (P36675) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RS3_ECOLI
Isoform —
PDB entities 3
Chains and sequence ranges Author chain c; PDBConstruct 1–233; UniProt 1–233

30S ribosomal protein S4

OrganismNot specified

UniProt P0A7V8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 16S rRNA × 1 23S rRNA × 1 30S ribosomal protein S3 × 1 (P0A7V3) 30S ribosomal protein S5 × 1 (P0A7W1) mRNA × 1 P-site tRNA fMet × 1 30S ribosomal protein S12 × 1 (P0A7S3) Peptide chain release factor 2 × 1 (P07012) Alternative ribosome-rescue factor A × 1 (P36675) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RS4_ECOLI
Isoform —
PDB entities 4
Chains and sequence ranges Author chain d; PDBConstruct 1–206; UniProt 1–206

30S ribosomal protein S5

OrganismNot specified

UniProt P0A7W1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 16S rRNA × 1 23S rRNA × 1 30S ribosomal protein S3 × 1 (P0A7V3) 30S ribosomal protein S4 × 1 (P0A7V8) mRNA × 1 P-site tRNA fMet × 1 30S ribosomal protein S12 × 1 (P0A7S3) Peptide chain release factor 2 × 1 (P07012) Alternative ribosome-rescue factor A × 1 (P36675) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RS5_ECOLI
Isoform —
PDB entities 5
Chains and sequence ranges Author chain e; PDBConstruct 1–167; UniProt 1–167

30S ribosomal protein S12

OrganismNot specified

UniProt P0A7S3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 16S rRNA × 1 23S rRNA × 1 30S ribosomal protein S3 × 1 (P0A7V3) 30S ribosomal protein S4 × 1 (P0A7V8) 30S ribosomal protein S5 × 1 (P0A7W1) mRNA × 1 P-site tRNA fMet × 1 Peptide chain release factor 2 × 1 (P07012) Alternative ribosome-rescue factor A × 1 (P36675) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RS12_ECOLI
Isoform —
PDB entities 8
Chains and sequence ranges Author chain l; PDBConstruct 1–124; UniProt 1–124

Peptide chain release factor 2

Escherichia coli

UniProt P07012

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 16S rRNA × 1 23S rRNA × 1 30S ribosomal protein S3 × 1 (P0A7V3) 30S ribosomal protein S4 × 1 (P0A7V8) 30S ribosomal protein S5 × 1 (P0A7W1) mRNA × 1 P-site tRNA fMet × 1 30S ribosomal protein S12 × 1 (P0A7S3) Alternative ribosome-rescue factor A × 1 (P36675) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RF2_ECOLI
Isoform —
PDB entities 9
Chains and sequence ranges Author chain v; PDBConstruct 19–383; UniProt 1–365

Alternative ribosome-rescue factor A

Escherichia coli

UniProt P36675

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 6 RNA 4 16S rRNA × 1 23S rRNA × 1 30S ribosomal protein S3 × 1 (P0A7V3) 30S ribosomal protein S4 × 1 (P0A7V8) 30S ribosomal protein S5 × 1 (P0A7W1) mRNA × 1 P-site tRNA fMet × 1 30S ribosomal protein S12 × 1 (P0A7S3) Peptide chain release factor 2 × 1 (P07012) Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name ARFA_ECOLI
Isoform —
PDB entities 10
Chains and sequence ranges Author chain w; PDBConstruct 3–57; UniProt 1–55

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id5u4j
Deposition date deposition_date2016-12-04
Structure title titleStructural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome
Keywords keywordsRibosome, ArfA, RF2, nonstop translation; RIBOSOME
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5u4j__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5u4j__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5u4j__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)33.85 Å
Rg (electron density)33.76 Å
Total Rg34.19 Å
Atom count11360
Residues853
Excluded volume175270 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5u4j__assembly_1__model_1 decameric (10) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id5u4je01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily20 —
Domain ID domain_id5u4je02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5u4jl00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
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7. Citations (1)