› 4v7p

X-ray diffraction
3.62Å resolution

Recognition of the amber stop codon by release factor RF1.

Released:
DOI: 10.2210/pdb4v7p/pdb
Model geometry
Fit model/data
PDB entry 4v7p coloured by chain, front view.
PDB entry 4v7p coloured by chain, side view.
PDB entry 4v7p coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Primary publication:
Recognition of the amber UAG stop codon by release factor RF1.
Korostelev A, Zhu J, Asahara H, Noller HF
EMBO J 29 2577-85 (2010)
PMID: 20588254

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-158444 (preferred)
Entry contents:
50 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (56 distinct):
Small ribosomal subunit protein uS2 Chains: AB, DB
Molecule details ›
Chains: AB, DB
Length: 234 amino acids
Theoretical weight: 26.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 7-240; Coverage: 91%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AC, DC
Molecule details ›
Chains: AC, DC
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 2-207; Coverage: 86%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, DD
Small ribosomal subunit protein uS5 Chains: AE, DE
Small ribosomal subunit protein bS6 Chains: AF, DF
Small ribosomal subunit protein uS7 Chains: AG, DG
Small ribosomal subunit protein uS8 Chains: AH, DH
Small ribosomal subunit protein uS9 Chains: AI, DI
Small ribosomal subunit protein uS10 Chains: AJ, DJ
Small ribosomal subunit protein uS11 Chains: AK, DK
Small ribosomal subunit protein uS12 Chains: AL, DL
Small ribosomal subunit protein uS13 Chains: AM, DM
Small ribosomal subunit protein uS14 Chains: AN, DN
Small ribosomal subunit protein uS15 Chains: AO, DO
Small ribosomal subunit protein bS16 Chains: AP, DP
Small ribosomal subunit protein uS17 Chains: AQ, DQ
Small ribosomal subunit protein bS18 Chains: AR, DR
Small ribosomal subunit protein uS19 Chains: AS, DS
Small ribosomal subunit protein bS20 Chains: AT, DT
Small ribosomal subunit protein bTHX Chains: AU, DU
Peptide chain release factor 1 Chains: AV, DV
Large ribosomal subunit protein uL2 Chains: BC, CC
Large ribosomal subunit protein uL3 Chains: BD, CD
Large ribosomal subunit protein uL4 Chains: BE, CE
Large ribosomal subunit protein uL5 Chains: BF, CF
Large ribosomal subunit protein uL6 Chains: BG, CG
Large ribosomal subunit protein bL9 Chains: BH, CH
Large ribosomal subunit protein uL10 Chains: BI, CI
Large ribosomal subunit protein uL13 Chains: BJ, CJ
Large ribosomal subunit protein uL14 Chains: BK, CK
Large ribosomal subunit protein uL15 Chains: BL, CL
Large ribosomal subunit protein uL16 Chains: BM, CM
Large ribosomal subunit protein bL17 Chains: BN, CN
Large ribosomal subunit protein uL18 Chains: BO, CO
Large ribosomal subunit protein bL19 Chains: BP, CP
Large ribosomal subunit protein bL20 Chains: BQ, CQ
Large ribosomal subunit protein bL21 Chains: BR, CR
Large ribosomal subunit protein uL22 Chains: BS, CS
Large ribosomal subunit protein uL23 Chains: BT, CT
Large ribosomal subunit protein uL24 Chains: BU, CU
Large ribosomal subunit protein bL25 Chains: BV, CV
Large ribosomal subunit protein bL27 Chains: BW, CW
Large ribosomal subunit protein bL28 Chains: BX, CX
Large ribosomal subunit protein uL29 Chains: BY, CY
Large ribosomal subunit protein uL30 Chains: BZ, CZ
Large ribosomal subunit protein bL31 Chains: B1, C1
Large ribosomal subunit protein bL32 Chains: B2, C2
Large ribosomal subunit protein bL33 Chains: B3, C3
Large ribosomal subunit protein bL34 Chains: B4, C4
Large ribosomal subunit protein bL35 Chains: B5, C5
16S ribosomal RNA Chains: AA, DA
P-site tRNA-fMet Chains: AW, DW
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3') Chain: AX
23S ribosomal RNA Chains: BA, CA
5S ribosomal RNA Chains: BB, CB
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3') Chain: DX

Ligands and Environments

2 bound ligands:
Ligand MG 410 x MG
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 210.38Å b: 452.7Å c: 617.09Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.26 0.26 0.291

Quick links

Citations

13 review citations

Translation in Prokaryotes.
Rodnina MV. (2018)
12 more

6 mentions without citation

Dynamics of ribosomes and release factors during translation termination in E. coli.
Adio et al. (2018)
5 more