› 5e7k

X-ray diffraction
3.2Å resolution

Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site

Released:
DOI: 10.2210/pdb5e7k/pdb
PDB entry 5e7k coloured by chain, front view.
PDB entry 5e7k coloured by chain, side view.
PDB entry 5e7k coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
Rozov A, Demeshkina N, Khusainov I, Westhof E, Yusupov M, Yusupova G
Nat Commun 7 10457 (2016)
PMID: 26791911

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero 55-mer (preferred)
hetero 54-mer
PDBe Complex ID:
PDB-CPX-148009 (preferred)
Entry contents:
48 distinct polypeptide molecules
9 distinct RNA molecules
Macromolecules (57 distinct):
Small ribosomal subunit protein uS2 Chains: 12, 1E
Molecule details ›
Chains: 12, 1E
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: 22, 2E
Molecule details ›
Chains: 22, 2E
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: 32, 3E
Molecule details ›
Chains: 32, 3E
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chains: 42, 4E
Molecule details ›
Chains: 42, 4E
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: 52, 5E
Molecule details ›
Chains: 52, 5E
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: 62, 6E
Molecule details ›
Chains: 62, 6E
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S ribosomal protein S8 Chains: 72, 7E
Molecule details ›
Chains: 72, 7E
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein uS9 Chains: 82, 8E
Molecule details ›
Chains: 82, 8E
Length: 128 amino acids
Theoretical weight: 14.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chains: 1A, 1I
Molecule details ›
Chains: 1A, 1I
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: 2A, 2I
Molecule details ›
Chains: 2A, 2I
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: 3A, 3I
Molecule details ›
Chains: 3A, 3I
Length: 132 amino acids
Theoretical weight: 14.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: 4A, 4I
Molecule details ›
Chains: 4A, 4I
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 1-126; Coverage: 100%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 type Z Chains: 5A, 5I
Molecule details ›
Chains: 5A, 5I
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein uS15 Chains: 6A, 6I
Molecule details ›
Chains: 6A, 6I
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chains: 7A, 7I
Molecule details ›
Chains: 7A, 7I
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: 8A, 8I
Molecule details ›
Chains: 8A, 8I
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
Small ribosomal subunit protein bS18 Chains: 9A, 9I
Molecule details ›
Chains: 9A, 9I
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: AA, AI
Molecule details ›
Chains: AA, AI
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: BA, BI
Molecule details ›
Chains: BA, BI
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bTHX Chains: 1B, 1F
Molecule details ›
Chains: 1B, 1F
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Large ribosomal subunit protein uL1 Chains: 71, 79
Molecule details ›
Chains: 71, 79
Length: 229 amino acids
Theoretical weight: 24.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 1-229; Coverage: 100%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chains: 11, 19
Molecule details ›
Chains: 11, 19
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: 21, 29
Molecule details ›
Chains: 21, 29
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: 31, 39
Molecule details ›
Chains: 31, 39
Length: 210 amino acids
Theoretical weight: 23.27 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-210; Coverage: 100%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: 41, 49
Molecule details ›
Chains: 41, 49
Length: 182 amino acids
Theoretical weight: 21.06 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ0 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chains: 51, 59
Molecule details ›
Chains: 51, 59
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB8
Large ribosomal subunit protein bL9 Chains: 61, 69
Molecule details ›
Chains: 61, 69
Length: 148 amino acids
Theoretical weight: 16.42 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-148; Coverage: 100%)
Gene names: TTHA0242, rplI
Sequence domains:
Large ribosomal subunit protein uL13 Chains: 15, 58
Molecule details ›
Chains: 15, 58
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chains: 25, 68
Molecule details ›
Chains: 25, 68
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: 35, 78
Molecule details ›
Chains: 35, 78
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-150; Coverage: 100%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chains: 45, 88
Molecule details ›
Chains: 45, 88
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: 55, 98
Molecule details ›
Chains: 55, 98
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chains: 65, A8
Molecule details ›
Chains: 65, A8
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 1-112; Coverage: 100%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: 75, B8
Molecule details ›
Chains: 75, B8
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-146; Coverage: 100%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chains: 85, C8
Molecule details ›
Chains: 85, C8
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chains: 95, D8
Molecule details ›
Chains: 95, D8
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: A5, E8
Molecule details ›
Chains: A5, E8
Length: 113 amino acids
Theoretical weight: 12.81 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: B5, F8
Molecule details ›
Chains: B5, F8
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-96; Coverage: 100%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chains: C5, G8
Molecule details ›
Chains: C5, G8
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-110; Coverage: 100%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: D5, H8
Molecule details ›
Chains: D5, H8
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
Large ribosomal subunit protein bL27 Chains: E5, I8
Molecule details ›
Chains: E5, I8
Length: 85 amino acids
Theoretical weight: 9.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: F5, J8
Molecule details ›
Chains: F5, J8
Length: 98 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: G5, K8
Molecule details ›
Chains: G5, K8
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: H5, L8
Molecule details ›
Chains: H5, L8
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31 Chain: M8
Molecule details ›
Chain: M8
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-71; Coverage: 100%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chains: J5, N8
Molecule details ›
Chains: J5, N8
Length: 60 amino acids
Theoretical weight: 6.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL34 Chains: L5, P8
Molecule details ›
Chains: L5, P8
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chains: M5, Q8
Molecule details ›
Chains: M5, Q8
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-65; Coverage: 100%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
16S ribosomal RNA Chains: 13, 1G
Molecule details ›
Chains: 13, 1G
Length: 1522 nucleotides
Theoretical weight: 494 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
tRNALys Chain: 1K
Molecule details ›
Chain: 1K
Length: 75 nucleotides
Theoretical weight: 24.25 KDa
Sequence domains: tRNA
tRNAfMet Chains: 2K, 2L
Molecule details ›
Chains: 2K, 2L
Length: 77 nucleotides
Theoretical weight: 24.86 KDa
Sequence domains: tRNA
tRNALys Chain: 3K
Molecule details ›
Chain: 3K
Length: 76 nucleotides
Theoretical weight: 24.38 KDa
Sequence domains: tRNA
Messenger RNA Chains: 4K, 4L
Molecule details ›
Chains: 4K, 4L
Length: 27 nucleotides
Theoretical weight: 8.89 KDa
23S ribosomal RNA Chains: 14, 1H
Molecule details ›
Chains: 14, 1H
Length: 2917 nucleotides
Theoretical weight: 948.54 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: 16, 1J
Molecule details ›
Chains: 16, 1J
Length: 122 nucleotides
Theoretical weight: 39.54 KDa
Sequence domains: 5S ribosomal RNA
tRNALys Chain: 1L
Molecule details ›
Chain: 1L
Length: 76 nucleotides
Theoretical weight: 24.6 KDa
Sequence domains: tRNA
tRNALys Chain: 3L
Molecule details ›
Chain: 3L
Length: 76 nucleotides
Theoretical weight: 24.39 KDa
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
Ligand MG 1138 x MG
Ligand SF4 2 x SF4
Ligand ZN 4 x ZN
7 modified residues:
Ligand U8U 2 x U8U
Ligand T6A 2 x T6A
Ligand PSU 8 x PSU
Ligand 5MU 5 x 5MU
Ligand 4SU 2 x 4SU
Ligand OMC 2 x OMC
Ligand G7M 2 x G7M

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 209.5Å b: 450.1Å c: 621.6Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.258

Quick links

Citations

21 review citations

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.
Atkins et al. (2016)
20 more

3 mentions without citation

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.
Rozov et al. (2016)
2 more