› 4v9n

X-ray diffraction
3.4Å resolution

Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.

Released:
DOI: 10.2210/pdb4v9n/pdb
Model geometry
Fit model/data
PDB entry 4v9n coloured by chain, front view.
PDB entry 4v9n coloured by chain, side view.
PDB entry 4v9n coloured by chain, top view.
Source organism: Thermus thermophilus HB27
Primary publication:
Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2.
Santos N, Zhu J, Donohue JP, Korostelev AA, Noller HF
Structure 21 1258-63 (2013)
PMID: 23769667

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-290010 (preferred)
Entry contents:
50 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (55 distinct):
Peptide chain release factor 2 Chains: AY, CY
Molecule details ›
Chains: AY, CY
Length: 362 amino acids
Theoretical weight: 40.89 KDa
Source organism: Thermus thermophilus HB27
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q72GJ6 (Residues: 17-378; Coverage: 96%)
Gene names: TT_C1852, prfB
Sequence domains:
Small ribosomal subunit protein uS2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
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, CC
Small ribosomal subunit protein uS4 Chains: AD, CD
Small ribosomal subunit protein uS5 Chains: AE, CE
Small ribosomal subunit protein bS6 Chains: AF, CF
Small ribosomal subunit protein uS7 Chains: AG, CG
Small ribosomal subunit protein uS8 Chains: AH, CH
Small ribosomal subunit protein uS9 Chains: AI, CI
Small ribosomal subunit protein uS10 Chains: AJ, CJ
Small ribosomal subunit protein uS11 Chains: AK, CK
Small ribosomal subunit protein uS12 Chains: AL, CL
Small ribosomal subunit protein uS13 Chains: AM, CM
Small ribosomal subunit protein uS14 Chains: AN, CN
Small ribosomal subunit protein uS15 Chains: AO, CO
Small ribosomal subunit protein bS16 Chains: AP, CP
Small ribosomal subunit protein uS17 Chains: AQ, CQ
Small ribosomal subunit protein bS18 Chains: AR, CR
Small ribosomal subunit protein uS19 Chains: AS, CS
Small ribosomal subunit protein bS20 Chains: AT, CT
Small ribosomal subunit protein bTHX Chains: AU, CU
Large ribosomal subunit protein uL2 Chains: BD, DD
Large ribosomal subunit protein uL3 Chains: BE, DE
Large ribosomal subunit protein uL4 Chains: BF, DF
Large ribosomal subunit protein uL5 Chains: BG, DG
Large ribosomal subunit protein uL6 Chains: BH, DH
Large ribosomal subunit protein bL9 Chains: BI, DI
Large ribosomal subunit protein uL11 Chains: BK, DK
Large ribosomal subunit protein uL13 Chains: BN, DN
Large ribosomal subunit protein uL14 Chains: BO, DO
Large ribosomal subunit protein uL15 Chains: BP, DP
Large ribosomal subunit protein uL16 Chains: BQ, DQ
Large ribosomal subunit protein bL17 Chains: BR, DR
Large ribosomal subunit protein uL18 Chains: BS, DS
Large ribosomal subunit protein bL19 Chains: BT, DT
Large ribosomal subunit protein bL20 Chains: BU, DU
Large ribosomal subunit protein bL21 Chains: BV, DV
Large ribosomal subunit protein uL22 Chains: BW, DW
Large ribosomal subunit protein uL23 Chains: BX, DX
Large ribosomal subunit protein uL24 Chains: BY, DY
Large ribosomal subunit protein bL25 Chains: BZ, DZ
Large ribosomal subunit protein bL27 Chains: B0, D0
Large ribosomal subunit protein bL28 Chains: B1, D1
Large ribosomal subunit protein uL29 Chains: B2, D2
Large ribosomal subunit protein uL30 Chains: B3, D3
Large ribosomal subunit protein bL31 Chains: B4, D4
Large ribosomal subunit protein bL32 Chains: B5, D5
Large ribosomal subunit protein bL33 Chains: B6, D6
Large ribosomal subunit protein bL34 Chains: B7, D7
Large ribosomal subunit protein bL35 Chains: B8, D8
16S ribosomal RNA Chains: AA, CA
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3') Chains: AV, CV
P-site tRNA-fMet Chains: AW, CW
23S ribosomal RNA Chains: BA, DA
5S ribosomal RNA Chains: BB, DB

Ligands and Environments

2 bound ligands:
Ligand MG 2410 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: SSRL BEAMLINE BL7-1, ALS BEAMLINE 12.3.1, SSRL BEAMLINE BL9-1, SSRL BEAMLINE BL11-1
Spacegroup: P212121
Unit cell:
a: 212.07Å b: 454.4Å c: 618.45Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.234 0.268
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

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

1 mention without citation

Inhibition of translation termination by small molecules targeting ribosomal release factors.
Ge et al. (2019)