PDBe 6n9f

X-ray diffraction
3.7Å resolution

Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic ACCA-DPhe and bound to mRNA and P-site tRNA at 3.7A resolution

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
Entry contents:
49 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (55 distinct):
50S Ribosomal Protein L2 Chains: 1D, 2D
Molecule details ›
Chains: 1D, 2D
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L3 Chains: 1E, 2E
Molecule details ›
Chains: 1E, 2E
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L4 Chains: 1F, 2F
Molecule details ›
Chains: 1F, 2F
Length: 210 amino acids
Theoretical weight: 23.27 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L5 Chains: 1G, 2G
Molecule details ›
Chains: 1G, 2G
Length: 182 amino acids
Theoretical weight: 21.06 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L6 Chains: 1H, 2H
Molecule details ›
Chains: 1H, 2H
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L9 Chains: 1I, 2I
Molecule details ›
Chains: 1I, 2I
Length: 148 amino acids
Theoretical weight: 16.42 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L13 Chains: 1N, 2N
Molecule details ›
Chains: 1N, 2N
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L14 Chains: 1O, 2O
Molecule details ›
Chains: 1O, 2O
Length: 122 amino acids
Theoretical weight: 13.32 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L15 Chains: 1P, 2P
Molecule details ›
Chains: 1P, 2P
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L16 Chains: 1Q, 2Q
Molecule details ›
Chains: 1Q, 2Q
Length: 141 amino acids
Theoretical weight: 15.99 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L17 Chains: 1R, 2R
Molecule details ›
Chains: 1R, 2R
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L18 Chains: 1S, 2S
Molecule details ›
Chains: 1S, 2S
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L19 Chains: 1T, 2T
Molecule details ›
Chains: 1T, 2T
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L20 Chains: 1U, 2U
Molecule details ›
Chains: 1U, 2U
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L21 Chains: 1V, 2V
Molecule details ›
Chains: 1V, 2V
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L22 Chains: 1W, 2W
Molecule details ›
Chains: 1W, 2W
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L23 Chains: 1X, 2X
Molecule details ›
Chains: 1X, 2X
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus
50S ribosomal protein L24 Chains: 1Y, 2Y
Molecule details ›
Chains: 1Y, 2Y
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW Q56435 (Residues: 1-110; Coverage: 100%)
Gene names: rpl24, rplX
Sequence domains:
50S ribosomal protein L25 Chains: 1Z, 2Z
Molecule details ›
Chains: 1Z, 2Z
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW Q72IA7 (Residues: 1-206; Coverage: 100%)
Gene names: TT_C1225, ctc, rplY
Sequence domains:
50S ribosomal protein L27 Chains: 10, 20
Molecule details ›
Chains: 10, 20
Length: 85 amino acids
Theoretical weight: 9.53 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
50S ribosomal protein L28 Chains: 11, 21
Molecule details ›
Chains: 11, 21
Length: 98 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: 12, 22
Molecule details ›
Chains: 12, 22
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW Q72I12 (Residues: 1-72; Coverage: 100%)
Gene names: TT_C1320, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: 13, 23
Molecule details ›
Chains: 13, 23
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P74909 (Residues: 1-60; Coverage: 100%)
Gene names: rpl30, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chains: 14, 24
Molecule details ›
Chains: 14, 24
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW Q72JR0 (Residues: 1-71; Coverage: 100%)
Gene names: TT_C0708, rpmE
Sequence domains: Ribosomal protein L31
50S ribosomal protein L32 Chains: 15, 25
Molecule details ›
Chains: 15, 25
Length: 60 amino acids
Theoretical weight: 6.72 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: 16, 26
Molecule details ›
Chains: 16, 26
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW Q72GW3 (Residues: 1-54; Coverage: 100%)
Gene names: TT_C1735, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: 17, 27
Molecule details ›
Chains: 17, 27
Length: 49 amino acids
Theoretical weight: 6.13 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P80340 (Residues: 1-49; Coverage: 100%)
Gene names: TTHA0446, rpl34, rpmH
Sequence domains: Ribosomal protein L34
50S Ribosomal Protein L35 Chains: 18, 28
Molecule details ›
Chains: 18, 28
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus
50S Ribosomal Protein L36 Chains: 19, 29
Molecule details ›
Chains: 19, 29
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S2 Chains: 1b, 2b
Molecule details ›
Chains: 1b, 2b
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S3 Chains: 1c, 2c
Molecule details ›
Chains: 1c, 2c
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S4 Chains: 1d, 2d
Molecule details ›
Chains: 1d, 2d
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S5 Chains: 1e, 2e
Molecule details ›
Chains: 1e, 2e
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S6 Chains: 1f, 2f
Molecule details ›
Chains: 1f, 2f
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S7 Chains: 1g, 2g
Molecule details ›
Chains: 1g, 2g
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S8 Chains: 1h, 2h
Molecule details ›
Chains: 1h, 2h
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus
30S ribosomal protein S9 Chains: 1i, 2i
Molecule details ›
Chains: 1i, 2i
Length: 128 amino acids
Theoretical weight: 14.41 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chains: 1j, 2j
Molecule details ›
Chains: 1j, 2j
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P80375 (Residues: 1-105; Coverage: 100%)
Gene names: rps10, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: 1k, 2k
Molecule details ›
Chains: 1k, 2k
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P62654 (Residues: 1-129; Coverage: 100%)
Gene names: TT_C1302, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: 1l, 2l
Molecule details ›
Chains: 1l, 2l
Length: 132 amino acids
Theoretical weight: 14.68 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P17293 (Residues: 1-132; Coverage: 100%)
Gene names: rps12, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: 1m, 2m
Molecule details ›
Chains: 1m, 2m
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P62655 (Residues: 1-126; Coverage: 100%)
Gene names: TT_C1303, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S14 type Z Chains: 1n, 2n
Molecule details ›
Chains: 1n, 2n
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P24320 (Residues: 1-61; Coverage: 100%)
Gene names: rps14, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
30S ribosomal protein S15 Chains: 1o, 2o
Molecule details ›
Chains: 1o, 2o
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P80378 (Residues: 1-89; Coverage: 100%)
Gene names: rps15, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: 1p, 2p
Molecule details ›
Chains: 1p, 2p
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P62238 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C0673, rps16, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: 1q, 2q
Molecule details ›
Chains: 1q, 2q
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P0DOY7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: 1r, 2r
Molecule details ›
Chains: 1r, 2r
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P62659 (Residues: 1-88; Coverage: 100%)
Gene names: TT_C1742, rps18, rpsR
Sequence domains: Ribosomal protein S18
30S Ribosomal Protein S19 Chains: 1s, 2s
Molecule details ›
Chains: 1s, 2s
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus
30S Ribosomal Protein S20 Chains: 1t, 2t
Molecule details ›
Chains: 1t, 2t
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus
30S ribosomal protein Thx Chains: 1u, 2u
Molecule details ›
Chains: 1u, 2u
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: NEW P62612 (Residues: 1-27; Coverage: 100%)
Gene name: rpsU
Sequence domains: 30S ribosomal protein Thx
23S ribosomal RNA Chains: 1A, 2A
Molecule details ›
Chains: 1A, 2A
Length: 2915 nucleotides
Theoretical weight: 948.04 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: 1B, 2B
Molecule details ›
Chains: 1B, 2B
Length: 121 nucleotides
Theoretical weight: 39.19 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: 1a, 2a
Molecule details ›
Chains: 1a, 2a
Length: 1521 nucleotides
Theoretical weight: 493.86 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chains: 1v, 2v
Molecule details ›
Chains: 1v, 2v
Length: 24 nucleotides
Theoretical weight: 7.8 KDa
ACCA-DPhe Chains: 1w, 2w
Molecule details ›
Chains: 1w, 2w
Length: 4 nucleotides
Theoretical weight: 1.37 KDa
P-site tRNA, Deacylated Initiator Methionyl-tRNA Chains: 1x, 2x
Molecule details ›
Chains: 1x, 2x
Length: 77 nucleotides
Theoretical weight: 24.85 KDa
Sequence domains: tRNA

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 211.39Å b: 452.15Å c: 617.64Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.238 0.236 0.279