› 4v9l

X-ray diffraction
3.5Å resolution

70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state.

Released:
DOI: 10.2210/pdb4v9l/pdb
PDB entry 4v9l coloured by chain, front view.
PDB entry 4v9l coloured by chain, side view.
PDB entry 4v9l coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.
Zhou J, Lancaster L, Donohue JP, Noller HF
Science 340 1236086 (2013)
PMID: 23812722

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 61-mer (preferred)
PDBe Complex ID:
PDB-CPX-216756 (preferred)
Entry contents:
55 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (60 distinct):
Small ribosomal subunit protein uS2 Chains: AB, CB
Molecule details ›
Chains: AB, CB
Length: 235 amino acids
Theoretical weight: 27.12 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62662 (Residues: 7-241; Coverage: 92%)
Gene names: TT_C0509, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
Length: 207 amino acids
Theoretical weight: 22.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62663 (Residues: 2-208; Coverage: 87%)
Gene names: TT_C1322, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, CD
Molecule details ›
Chains: AD, CD
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, CE
Molecule details ›
Chains: AE, CE
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, CF
Molecule details ›
Chains: AF, CF
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, CG
Molecule details ›
Chains: AG, CG
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, CH
Molecule details ›
Chains: AH, CH
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, CI
Molecule details ›
Chains: AI, CI
Length: 127 amino acids
Theoretical weight: 14.28 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, CJ
Molecule details ›
Chains: AJ, CJ
Length: 99 amino acids
Theoretical weight: 11.4 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62653 (Residues: 3-101; Coverage: 94%)
Gene names: TT_C1329, rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: AK, CK
Molecule details ›
Chains: AK, CK
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, CL
Molecule details ›
Chains: AL, CL
Length: 125 amino acids
Theoretical weight: 13.88 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P61941 (Residues: 2-126; Coverage: 95%)
Gene names: TT_C1333, rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: AM, CM
Molecule details ›
Chains: AM, CM
Length: 125 amino acids
Theoretical weight: 14.21 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62655 (Residues: 2-126; Coverage: 99%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: AN, CN
Molecule details ›
Chains: AN, CN
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, CO
Molecule details ›
Chains: AO, CO
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, CP
Molecule details ›
Chains: AP, CP
Length: 84 amino acids
Theoretical weight: 10 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62238 (Residues: 1-84; Coverage: 96%)
Gene names: TT_C0673, rps16, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: AQ, CQ
Molecule details ›
Chains: AQ, CQ
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62658 (Residues: 2-101; Coverage: 95%)
Gene names: TT_C1319, rps17, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: AR, CR
Molecule details ›
Chains: AR, CR
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, CS
Molecule details ›
Chains: AS, CS
Length: 79 amino acids
Theoretical weight: 9.01 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62660 (Residues: 4-82; Coverage: 85%)
Gene names: TT_C1324, rps19, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: AT, CT
Molecule details ›
Chains: AT, CT
Length: 99 amino acids
Theoretical weight: 10.92 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
Elongation factor G Chains: AY, CY
Molecule details ›
Chains: AY, CY
Length: 687 amino acids
Theoretical weight: 76.55 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN5 (Residues: 4-690; Coverage: 99%)
Gene names: TTHA1695, fus, fusA
Sequence domains:
VIOMYCIN Chains: AU, CU
Molecule details ›
Chains: AU, CU
Length: 6 amino acids
Theoretical weight: 704 Da
Source organism: Streptomyces
Large ribosomal subunit protein uL1 Chains: BC, DC
Molecule details ›
Chains: BC, DC
Length: 228 amino acids
Theoretical weight: 24.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GV9 (Residues: 2-229; Coverage: 100%)
Gene names: TT_C1739, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chains: BD, DD
Molecule details ›
Chains: BD, DD
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: BE, DE
Molecule details ›
Chains: BE, DE
Length: 205 amino acids
Theoretical weight: 22.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I04 (Residues: 1-205; Coverage: 100%)
Gene names: TT_C1328, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: BF, DF
Molecule details ›
Chains: BF, DF
Length: 208 amino acids
Theoretical weight: 23.07 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I05 (Residues: 2-203; Coverage: 99%)
Gene names: TT_C1327, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: BG, DG
Molecule details ›
Chains: BG, DG
Length: 181 amino acids
Theoretical weight: 20.93 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ0 (Residues: 2-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chains: BH, DH
Molecule details ›
Chains: BH, DH
Length: 167 amino acids
Theoretical weight: 18.09 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I19 (Residues: 12-178; Coverage: 93%)
Gene names: TT_C1313, rplF
Sequence domains: Ribosomal protein L6
50S RIBOSOMAL PROTEIN L10 Chains: BJ, DJ
Molecule details ›
Chains: BJ, DJ
Length: 170 amino acids
Theoretical weight: 14.49 KDa
Source organism: Thermus thermophilus HB27
Large ribosomal subunit protein uL11 Chains: BK, DK
Molecule details ›
Chains: BK, DK
Length: 140 amino acids
Theoretical weight: 14.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P62442 (Residues: 2-141; Coverage: 95%)
Gene names: TT_C1738, rplK
Sequence domains:
Large ribosomal subunit protein uL13 Chains: BN, DN
Molecule details ›
Chains: BN, DN
Length: 138 amino acids
Theoretical weight: 15.7 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IN1 (Residues: 1-138; Coverage: 99%)
Gene names: TT_C1101, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: BO, DO
Molecule details ›
Chains: BO, DO
Length: 122 amino acids
Theoretical weight: 13.32 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: BP, DP
Molecule details ›
Chains: BP, DP
Length: 146 amino acids
Theoretical weight: 15.86 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I23 (Residues: 5-150; Coverage: 97%)
Gene names: TT_C1309, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chains: BQ, DQ
Molecule details ›
Chains: BQ, DQ
Length: 141 amino acids
Theoretical weight: 15.99 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: BR, DR
Molecule details ›
Chains: BR, DR
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: BS, DS
Molecule details ›
Chains: BS, DS
Length: 99 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I20 (Residues: 11-109; Coverage: 88%)
Gene names: TT_C1312, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: BT, DT
Molecule details ›
Chains: BT, DT
Length: 138 amino acids
Theoretical weight: 16.29 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JU9 (Residues: 1-138; Coverage: 95%)
Gene names: TT_C0669, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: BU, DU
Molecule details ›
Chains: BU, DU
Length: 117 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72L76 (Residues: 2-118; Coverage: 99%)
Gene names: TT_C0185, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: BV, DV
Molecule details ›
Chains: BV, DV
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: BW, DW
Molecule details ›
Chains: BW, DW
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I09 (Residues: 1-113; Coverage: 100%)
Gene names: TT_C1323, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: BX, DX
Molecule details ›
Chains: BX, DX
Length: 93 amino acids
Theoretical weight: 10.39 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I06 (Residues: 3-95; Coverage: 97%)
Gene names: TT_C1326, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: BY, DY
Molecule details ›
Chains: BY, DY
Length: 107 amino acids
Theoretical weight: 11.7 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I15 (Residues: 2-108; Coverage: 97%)
Gene names: TT_C1317, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: BZ, DZ
Molecule details ›
Chains: BZ, DZ
Length: 185 amino acids
Theoretical weight: 20.88 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72IA7 (Residues: 3-187; Coverage: 90%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chains: B0, D0
Molecule details ›
Chains: B0, D0
Length: 84 amino acids
Theoretical weight: 9.4 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 uL29 Chains: B2, D2
Molecule details ›
Chains: B2, D2
Length: 71 amino acids
Theoretical weight: 8.54 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I12 (Residues: 2-72; Coverage: 99%)
Gene names: TT_C1320, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: B3, D3
Molecule details ›
Chains: B3, D3
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I22 (Residues: 1-60; Coverage: 100%)
Gene names: TT_C1310, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL32 Chains: B5, D5
Molecule details ›
Chains: B5, D5
Length: 59 amino acids
Theoretical weight: 6.59 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: B6, D6
Molecule details ›
Chains: B6, D6
Length: 50 amino acids
Theoretical weight: 6.21 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GW3 (Residues: 5-54; Coverage: 93%)
Gene names: TT_C1735, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: B7, D7
Molecule details ›
Chains: B7, D7
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: B8, D8
Molecule details ›
Chains: B8, D8
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
Large ribosomal subunit protein bL36 Chains: B9, D9
Molecule details ›
Chains: B9, D9
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72I28 (Residues: 1-37; Coverage: 100%)
Gene names: TT_C1304, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein bL12 Chains: Be, De
Molecule details ›
Chains: Be, De
Length: 102 amino acids
Theoretical weight: 10.2 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72GS2 (Residues: 51-122; Coverage: 58%)
Gene names: TT_C1776, rplL
Sequence domains: Ribosomal protein L7/L12 C-terminal domain
50S RIBOSOMAL PROTEIN L7/L12 Chains: Bf, Bg, Df, Dg
Molecule details ›
Chains: Bf, Bg, Df, Dg
Length: 31 amino acids
Theoretical weight: 2.66 KDa
Source organism: Thermus thermophilus HB27
50S RIBOSOMAL PROTEIN L7/L12 Chains: Bh, Dh
Molecule details ›
Chains: Bh, Dh
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Thermus thermophilus HB27
Large ribosomal subunit protein bL28 Chains: B1, D1
Molecule details ›
Chains: B1, D1
Length: 93 amino acids
Theoretical weight: 10.43 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72G84 (Residues: 3-95; Coverage: 95%)
Gene names: TT_C1964, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein bL31 Chains: B4, D4
Molecule details ›
Chains: B4, D4
Length: 35 amino acids
Theoretical weight: 3.89 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q72JR0 (Residues: 1-35; Coverage: 49%)
Gene names: TT_C0708, rpmE
Sequence domains: Ribosomal protein L31
16S ribosomal RNA Chains: AA, CA
Molecule details ›
Chains: AA, CA
Length: 1511 nucleotides
Theoretical weight: 490.59 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
transfer RNA Chains: AW, CW
Molecule details ›
Chains: AW, CW
Length: 77 nucleotides
Theoretical weight: 24.73 KDa
Sequence domains: tRNA
Messenger RNA Chains: AV, CV
Molecule details ›
Chains: AV, CV
Length: 23 nucleotides
Theoretical weight: 7.55 KDa
23S ribosomal RNA Chains: BA, DA
Molecule details ›
Chains: BA, DA
Length: 2879 nucleotides
Theoretical weight: 936.3 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: BB, DB
Molecule details ›
Chains: BB, DB
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand FUA 2 x FUA
Ligand GDP 2 x GDP
Ligand MG 2 x MG
3 modified residues:
Ligand KBE 2 x KBE
Ligand DPP 2 x DPP
Ligand 5OH 2 x 5OH

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D, ALS BEAMLINE 12.3.1
Spacegroup: C2
Unit cell:
a: 308.96Å b: 670.662Å c: 347.765Å
α: 90° β: 92.524° γ: 90°
R-values:
R R work R free
0.286 0.284 0.328

Quick links

Citations

23 review citations

Nucleolar stress with and without p53.
James et al. (2014)
22 more

6 mentions without citation

Interfacial inhibitors.
Pommier et al. (2015)
5 more