› 4v7p

X-ray diffraction
3.62Å resolution

Recognition of the amber stop codon by release factor RF1.

Released:
DOI: 10.2210/pdb4v7p/pdb
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
Molecule details ›
Chains: AD, DD
Length: 208 amino acids
Theoretical weight: 24.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62664 (Residues: 2-209; Coverage: 100%)
Gene names: TT_C1301, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: AE, DE
Molecule details ›
Chains: AE, DE
Length: 151 amino acids
Theoretical weight: 16.46 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62665 (Residues: 5-155; Coverage: 93%)
Gene names: TT_C1311, rps5, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: AF, DF
Molecule details ›
Chains: AF, DF
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62666 (Residues: 1-101; Coverage: 100%)
Gene names: TT_C1740, rps6, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chains: AG, DG
Molecule details ›
Chains: AG, DG
Length: 155 amino acids
Theoretical weight: 17.92 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62667 (Residues: 2-156; Coverage: 99%)
Gene names: TT_C1332, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chains: AH, DH
Molecule details ›
Chains: AH, DH
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62668 (Residues: 1-138; Coverage: 100%)
Gene names: TT_C1314, rps8, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chains: AI, DI
Molecule details ›
Chains: AI, DI
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62669 (Residues: 2-128; Coverage: 99%)
Gene names: TT_C1100, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: AJ, DJ
Molecule details ›
Chains: AJ, DJ
Length: 98 amino acids
Theoretical weight: 11.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62653 (Residues: 3-100; Coverage: 93%)
Gene names: TT_C1329, rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: AK, DK
Molecule details ›
Chains: AK, DK
Length: 119 amino acids
Theoretical weight: 12.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62654 (Residues: 11-129; Coverage: 92%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: AL, DL
Molecule details ›
Chains: AL, DL
Length: 124 amino acids
Theoretical weight: 13.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 2-125; Coverage: 94%)
Gene names: TT_C1333, rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: AM, DM
Molecule details ›
Chains: AM, DM
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62655 (Residues: 2-118; Coverage: 93%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: AN, DN
Molecule details ›
Chains: AN, DN
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62656 (Residues: 2-61; Coverage: 98%)
Gene names: TT_C1315, rps14, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: AO, DO
Molecule details ›
Chains: AO, DO
Length: 88 amino acids
Theoretical weight: 10.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62657 (Residues: 2-89; Coverage: 99%)
Gene names: TT_C0773, rps15, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: AP, DP
Molecule details ›
Chains: AP, DP
Length: 83 amino acids
Theoretical weight: 9.92 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62238 (Residues: 1-83; Coverage: 94%)
Gene names: TT_C0673, rps16, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: AQ, DQ
Molecule details ›
Chains: AQ, DQ
Length: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62658 (Residues: 2-100; Coverage: 94%)
Gene names: TT_C1319, rps17, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: AR, DR
Molecule details ›
Chains: AR, DR
Length: 70 amino acids
Theoretical weight: 8.16 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62659 (Residues: 19-88; Coverage: 80%)
Gene names: TT_C1742, rps18, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: AS, DS
Molecule details ›
Chains: AS, DS
Length: 78 amino acids
Theoretical weight: 8.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62660 (Residues: 4-81; Coverage: 84%)
Gene names: TT_C1324, rps19, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: AT, DT
Molecule details ›
Chains: AT, DT
Length: 99 amino acids
Theoretical weight: 10.91 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62661 (Residues: 8-106; Coverage: 93%)
Gene names: TT_C1031, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chains: AU, DU
Molecule details ›
Chains: AU, DU
Length: 24 amino acids
Theoretical weight: 2.96 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62613 (Residues: 2-25; Coverage: 89%)
Gene names: TT_C1030, rpsU
Sequence domains: 30S ribosomal protein Thx
Peptide chain release factor 1 Chains: AV, DV
Molecule details ›
Chains: AV, DV
Length: 354 amino acids
Theoretical weight: 40.15 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72HB8 (Residues: 1-354; Coverage: 100%)
Gene names: TT_C1577, prfA
Sequence domains:
Large ribosomal subunit protein uL2 Chains: BC, CC
Molecule details ›
Chains: BC, CC
Length: 275 amino acids
Theoretical weight: 30.4 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I07 (Residues: 2-276; Coverage: 100%)
Gene names: TT_C1325, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: BD, CD
Molecule details ›
Chains: BD, CD
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I04 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1328, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: BE, CE
Molecule details ›
Chains: BE, CE
Length: 205 amino acids
Theoretical weight: 22.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I05 (Residues: 1-205; Coverage: 100%)
Gene names: TT_C1327, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: BF, CF
Molecule details ›
Chains: BF, CF
Length: 181 amino acids
Theoretical weight: 20.94 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I16 (Residues: 2-182; Coverage: 100%)
Gene names: TT_C1316, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chains: BG, CG
Molecule details ›
Chains: BG, CG
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I19 (Residues: 1-180; Coverage: 100%)
Gene names: TT_C1313, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chains: BH, CH
Molecule details ›
Chains: BH, CH
Length: 148 amino acids
Theoretical weight: 16.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GV5 (Residues: 1-148; Coverage: 100%)
Gene names: TT_C1743, rplI
Sequence domains:
Large ribosomal subunit protein uL10 Chains: BI, CI
Molecule details ›
Chains: BI, CI
Length: 173 amino acids
Theoretical weight: 18.59 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GS1 (Residues: 1-173; Coverage: 100%)
Gene names: TT_C1777, rplJ
Sequence domains: Ribosomal protein L10
Large ribosomal subunit protein uL13 Chains: BJ, CJ
Molecule details ›
Chains: BJ, CJ
Length: 139 amino acids
Theoretical weight: 15.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IN1 (Residues: 2-140; Coverage: 99%)
Gene names: TT_C1101, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: BK, CK
Molecule details ›
Chains: BK, CK
Length: 122 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I14 (Residues: 1-122; Coverage: 100%)
Gene names: TT_C1318, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chains: BL, CL
Molecule details ›
Chains: BL, CL
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I23 (Residues: 1-150; Coverage: 100%)
Gene names: TT_C1309, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chains: BM, CM
Molecule details ›
Chains: BM, CM
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I11 (Residues: 1-141; Coverage: 100%)
Gene names: TT_C1321, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chains: BN, CN
Molecule details ›
Chains: BN, CN
Length: 117 amino acids
Theoretical weight: 13.62 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I33 (Residues: 2-118; Coverage: 99%)
Gene names: TT_C1299, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: BO, CO
Molecule details ›
Chains: BO, CO
Length: 111 amino acids
Theoretical weight: 12.51 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I20 (Residues: 2-112; Coverage: 99%)
Gene names: TT_C1312, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: BP, CP
Molecule details ›
Chains: BP, CP
Length: 146 amino acids
Theoretical weight: 17.22 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JU9 (Residues: 1-146; Coverage: 100%)
Gene names: TT_C0669, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: BQ, CQ
Molecule details ›
Chains: BQ, CQ
Length: 116 amino acids
Theoretical weight: 13.5 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L76 (Residues: 2-118; Coverage: 98%)
Gene names: TT_C0185, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: BR, CR
Molecule details ›
Chains: BR, CR
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72HR2 (Residues: 1-101; Coverage: 100%)
Gene names: TT_C1424, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chains: BS, CS
Molecule details ›
Chains: BS, CS
Length: 112 amino acids
Theoretical weight: 12.68 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I09 (Residues: 1-112; Coverage: 99%)
Gene names: TT_C1323, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: BT, CT
Molecule details ›
Chains: BT, CT
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I06 (Residues: 1-96; Coverage: 100%)
Gene names: TT_C1326, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: BU, CU
Molecule details ›
Chains: BU, CU
Length: 109 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I15 (Residues: 2-110; Coverage: 99%)
Gene names: TT_C1317, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: BV, CV
Molecule details ›
Chains: BV, CV
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IA7 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chains: BW, CW
Molecule details ›
Chains: BW, CW
Length: 84 amino acids
Theoretical weight: 9.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72HR3 (Residues: 2-85; Coverage: 99%)
Gene names: TT_C1423, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: BX, CX
Molecule details ›
Chains: BX, CX
Length: 98 amino acids
Theoretical weight: 11.03 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72G84 (Residues: 1-98; Coverage: 100%)
Gene names: TT_C1964, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: BY, CY
Molecule details ›
Chains: BY, CY
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I12 (Residues: 1-72; Coverage: 100%)
Gene names: TT_C1320, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: BZ, CZ
Molecule details ›
Chains: BZ, CZ
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I22 (Residues: 1-59; Coverage: 98%)
Gene names: TT_C1310, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chains: B1, C1
Molecule details ›
Chains: B1, C1
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JR0 (Residues: 1-71; Coverage: 100%)
Gene names: TT_C0708, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chains: B2, C2
Molecule details ›
Chains: B2, C2
Length: 59 amino acids
Theoretical weight: 6.6 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62652 (Residues: 2-60; Coverage: 98%)
Gene names: TT_C0050, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chains: B3, C3
Molecule details ›
Chains: B3, C3
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GW3 (Residues: 1-54; Coverage: 100%)
Gene names: TT_C1735, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: B4, C4
Molecule details ›
Chains: B4, C4
Length: 48 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80340 (Residues: 1-48; Coverage: 98%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: B5, C5
Molecule details ›
Chains: B5, C5
Length: 64 amino acids
Theoretical weight: 7.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L77 (Residues: 2-65; Coverage: 99%)
Gene names: TT_C0184, rpmI
Sequence domains: Ribosomal protein L35
16S ribosomal RNA Chains: AA, DA
Molecule details ›
Chains: AA, DA
Length: 1504 nucleotides
Theoretical weight: 488.43 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-site tRNA-fMet Chains: AW, DW
Molecule details ›
Chains: AW, DW
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3') Chain: AX
Molecule details ›
Chain: AX
Length: 7 nucleotides
Theoretical weight: 2.25 KDa
23S ribosomal RNA Chains: BA, CA
Molecule details ›
Chains: BA, CA
Length: 2879 nucleotides
Theoretical weight: 936.3 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: BB, CB
Molecule details ›
Chains: BB, CB
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3') Chain: DX
Molecule details ›
Chain: DX
Length: 9 nucleotides
Theoretical weight: 2.9 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
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