› 4v9i

X-ray diffraction
3.3Å resolution

Crystal structure of thermus thermophilus 70S in complex with tRNAs and mRNA containing a pseudouridine in a stop codon

Released:
DOI: 10.2210/pdb4v9i/pdb
PDB entry 4v9i coloured by chain, front view.
PDB entry 4v9i coloured by chain, side view.
PDB entry 4v9i coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Unusual base pairing during the decoding of a stop codon by the ribosome.
Fernández IS, Ng CL, Kelley AC, Wu G, Yu YT, Ramakrishnan V
Nature 500 107-10 (2013)
PMID: 23812587

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
PDBe Complex ID:
PDB-CPX-215956 (preferred)
Entry contents:
52 distinct polypeptide molecules
8 distinct RNA molecules
Macromolecules (60 distinct):
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 HB8
UniProt:
  • Canonical: P80371 (Residues: 7-240; Coverage: 91%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: AC, CC
Molecule details ›
Chains: AC, CC
Length: 206 amino acids
Theoretical weight: 22.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 2-207; Coverage: 86%)
Gene names: TTHA1686, 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 HB8
UniProt:
  • Canonical: P80373 (Residues: 2-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: AE, CE
Molecule details ›
Chains: AE, CE
Length: 150 amino acids
Theoretical weight: 16.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-154; Coverage: 93%)
Gene names: TTHA1675, 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 HB8
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, 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 HB8
UniProt:
  • Canonical: P17291 (Residues: 2-156; Coverage: 99%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S Ribosomal protein S8 Chains: AH, CH
Molecule details ›
Chains: AH, CH
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein uS9 Chains: AI, CI
Molecule details ›
Chains: AI, CI
Length: 127 amino acids
Theoretical weight: 14.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 2-128; Coverage: 99%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: AJ, CJ
Molecule details ›
Chains: AJ, CJ
Length: 98 amino acids
Theoretical weight: 11.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 3-100; Coverage: 93%)
Gene names: TTHA1693, 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 HB8
UniProt:
  • Canonical: P80376 (Residues: 11-129; Coverage: 92%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: AL, CL
Molecule details ›
Chains: AL, CL
Length: 124 amino acids
Theoretical weight: 13.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-125; Coverage: 94%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: AM, CM
Molecule details ›
Chains: AM, CM
Length: 124 amino acids
Theoretical weight: 14.08 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 2-125; Coverage: 98%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S Ribosomal protein S14 Chains: AN, CN
Molecule details ›
Chains: AN, CN
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
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 HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 2-89; Coverage: 99%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: AP, CP
Molecule details ›
Chains: AP, CP
Length: 83 amino acids
Theoretical weight: 9.92 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-83; Coverage: 94%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S Ribosomal protein S17 Chains: AQ, CQ
Molecule details ›
Chains: AQ, CQ
Length: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB8
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 HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 19-88; Coverage: 80%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: AS, CS
Molecule details ›
Chains: AS, CS
Length: 78 amino acids
Theoretical weight: 8.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 4-81; Coverage: 84%)
Gene names: TTHA1688, 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 HB8
UniProt:
  • Canonical: P80380 (Residues: 8-106; Coverage: 93%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chains: AU, CU
Molecule details ›
Chains: AU, CU
Length: 24 amino acids
Theoretical weight: 2.96 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-25; Coverage: 89%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
50S ribosomal protein L1 Chain: BC
Molecule details ›
Chain: BC
Length: 206 amino acids
Theoretical weight: 17.81 KDa
Source organism: Thermus thermophilus HB8
Large ribosomal subunit protein uL2 Chains: BD, DD
Molecule details ›
Chains: BD, DD
Length: 271 amino acids
Theoretical weight: 29.83 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 2-272; Coverage: 98%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: BE, DE
Molecule details ›
Chains: BE, DE
Length: 204 amino acids
Theoretical weight: 22.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-204; Coverage: 99%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: BF, DF
Molecule details ›
Chains: BF, DF
Length: 207 amino acids
Theoretical weight: 23.01 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-207; Coverage: 99%)
Gene names: TTHA1691, 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 HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 2-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chains: BH, DH
Molecule details ›
Chains: BH, DH
Length: 159 amino acids
Theoretical weight: 17.36 KDa
Source organism: Thermus thermophilus HB8
Large ribosomal subunit protein bL9 Chains: BI, DI
Molecule details ›
Chains: BI, DI
Length: 145 amino acids
Theoretical weight: 16.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-145; Coverage: 98%)
Gene names: TTHA0242, rplI
Sequence domains:
50S ribosomal protein L10 Chains: BJ, DJ
Molecule details ›
Chains: BJ, DJ
Length: 130 amino acids
Theoretical weight: 9.26 KDa
Source organism: Thermus thermophilus HB8
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 HB8
UniProt:
  • Canonical: P60488 (Residues: 1-138; Coverage: 99%)
Gene names: TTHA1465, 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 HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, 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 HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 5-150; Coverage: 97%)
Gene names: TTHA1673, 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 HB8
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, 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 HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 2-118; Coverage: 99%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: BS, DS
Molecule details ›
Chains: BS, DS
Length: 98 amino acids
Theoretical weight: 10.94 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 11-108; Coverage: 88%)
Gene names: TTHA1676, 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: 137 amino acids
Theoretical weight: 16.22 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-137; Coverage: 94%)
Gene names: TTHA1031, 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: 13.57 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 2-118; Coverage: 99%)
Gene names: TTHA0553, 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 HB8
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, 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: 12.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chains: BX, DX
Molecule details ›
Chains: BX, DX
Length: 92 amino acids
Theoretical weight: 10.27 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 3-94; Coverage: 96%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: BY, DY
Molecule details ›
Chains: BY, DY
Length: 100 amino acids
Theoretical weight: 11.08 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 2-101; Coverage: 91%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: BZ, DZ
Molecule details ›
Chains: BZ, DZ
Length: 176 amino acids
Theoretical weight: 19.89 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 3-178; Coverage: 85%)
Gene names: TTHA1589, rpl25, rplY, rptL5
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 HB8
UniProt:
  • Canonical: P60493 (Residues: 2-85; Coverage: 99%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: B1, D1
Molecule details ›
Chains: B1, D1
Length: 93 amino acids
Theoretical weight: 10.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 3-95; Coverage: 95%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
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 HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 2-72; Coverage: 99%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: B3, D3
Molecule details ›
Chains: B3, D3
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-59; Coverage: 98%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chains: B4, D4
Molecule details ›
Chains: B4, D4
Length: 30 amino acids
Theoretical weight: 3.28 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 10-39; Coverage: 42%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
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 HB8
UniProt:
  • Canonical: P80339 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33 Chains: B6, D6
Molecule details ›
Chains: B6, D6
Length: 44 amino acids
Theoretical weight: 5.47 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 9-52; Coverage: 82%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: B7, D7
Molecule details ›
Chains: B7, D7
Length: 48 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-48; Coverage: 98%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: B8, D8
Molecule details ›
Chains: B8, D8
Length: 63 amino acids
Theoretical weight: 7.25 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 2-64; Coverage: 97%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chains: B9, D9
Molecule details ›
Chains: B9, D9
Length: 36 amino acids
Theoretical weight: 4.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 2-37; Coverage: 97%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
50S Ribosomal protein L1 Chain: DC
Molecule details ›
Chain: DC
Length: 196 amino acids
Theoretical weight: 17.1 KDa
Source organism: Thermus thermophilus HB8
16S ribosomal RNA Chains: AA, CA
Molecule details ›
Chains: AA, CA
Length: 1504 nucleotides
Theoretical weight: 488.39 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
P-SITE tRNA Chains: AV, CV
Molecule details ›
Chains: AV, CV
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
E-SITE tRNA Chains: AW, CW
Molecule details ›
Chains: AW, CW
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Sequence domains: tRNA
A-SITE tRNA Chains: AY, CY
Molecule details ›
Chains: AY, CY
Length: 75 nucleotides
Theoretical weight: 24.43 KDa
Sequence domains: tRNA
Messenger RNA Chain: AX
Molecule details ›
Chain: AX
Length: 7 nucleotides
Theoretical weight: 2.25 KDa
23S ribosomal RNA Chains: BA, DA
Molecule details ›
Chains: BA, DA
Length: 2915 nucleotides
Theoretical weight: 947.92 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
Messenger RNA Chain: CX
Molecule details ›
Chain: CX
Length: 4 nucleotides
Theoretical weight: 1.24 KDa

Ligands and Environments

No bound ligands
1 modified residue:
Ligand PSU 1 x PSU

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 209.92Å b: 449.9Å c: 624.9Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.225 0.278

Quick links

Citations

57 review citations

Gene expression regulation mediated through reversible m⁶A RNA methylation.
Fu et al. (2014)
56 more

2 mentions without citation

Roadblocks and resolutions in eukaryotic translation.
Schuller et al. (2018)
1 more