PDBe 5d8b

X-ray diffraction
3.63Å resolution

Crystal structure of T. thermophilus ribosome containing a P-site wobble mismatch

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
Entry contents:
49 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (54 distinct):
50S ribosomal protein L2 Chains: A, WA
Molecule details ›
Chains: A, WA
Length: 271 amino acids
Theoretical weight: 29.83 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60405 (Residues: 2-272; Coverage: 98%)
Gene names: TTHA1689, rplB
Sequence domains:
50S ribosomal protein L3 Chains: B, XA
Molecule details ›
Chains: B, XA
Length: 206 amino acids
Theoretical weight: 22.45 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
50S ribosomal protein L4 Chains: C, YA
Molecule details ›
Chains: C, YA
Length: 205 amino acids
Theoretical weight: 22.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN9 (Residues: 6-210; Coverage: 98%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chains: D, ZA
Molecule details ›
Chains: D, ZA
Length: 182 amino acids
Theoretical weight: 21.08 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ0 (Residues: 1-182; Coverage: 100%)
Gene names: TTHA1680, rplE
Sequence domains:
50S ribosomal protein L6 Chains: AB, E
Molecule details ›
Chains: AB, E
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: A0A0M9ADP1 (Residues: 1-180; Coverage: 100%)
Gene names: BVI061214_01035, rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L9 Chains: BB, F
Molecule details ›
Chains: BB, F
Length: 148 amino acids
Theoretical weight: 16.44 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-148; Coverage: 100%)
Gene names: TTHA0242, rplI
Sequence domains:
50S ribosomal protein L11 Chains: CB, G
Molecule details ›
Chains: CB, G
Length: 147 amino acids
Theoretical weight: 15.53 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLP6 (Residues: 1-147; Coverage: 100%)
Gene names: TTHA0247, rplK
Sequence domains:
50S ribosomal protein L13 Chains: DB, H
Molecule details ›
Chains: DB, H
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: EB, I
Molecule details ›
Chains: EB, I
Length: 122 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
50S ribosomal protein L15 Chains: FB, J
Molecule details ›
Chains: FB, J
Length: 150 amino acids
Theoretical weight: 16.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ7 (Residues: 1-150; Coverage: 100%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chains: GB, K
Molecule details ›
Chains: GB, K
Length: 141 amino acids
Theoretical weight: 15.98 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60489 (Residues: 1-141; Coverage: 100%)
Gene names: TTHA1685, rplP
Sequence domains: Ribosomal protein L16p/L10e
50S ribosomal protein L17 Chains: HB, L
Molecule details ›
Chains: HB, L
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: IB, M
Molecule details ›
Chains: IB, M
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ4 (Residues: 1-112; Coverage: 100%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
50S ribosomal protein L19 Chains: JB, N
Molecule details ›
Chains: JB, N
Length: 146 amino acids
Theoretical weight: 17.22 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60490 (Residues: 1-146; Coverage: 100%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chains: KB, O
Molecule details ›
Chains: KB, O
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60491 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: LB, P
Molecule details ›
Chains: LB, P
Length: 101 amino acids
Theoretical weight: 11.07 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60492 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA1783, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
50S ribosomal protein L22 Chains: MB, Q
Molecule details ›
Chains: MB, Q
Length: 113 amino acids
Theoretical weight: 12.81 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-113; Coverage: 100%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chains: NB, R
Molecule details ›
Chains: NB, R
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-96; Coverage: 100%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: OB, S
Molecule details ›
Chains: OB, S
Length: 110 amino acids
Theoretical weight: 12.09 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP9 (Residues: 1-110; Coverage: 100%)
Gene names: TTHA1681, rplX
Sequence domains:
50S ribosomal protein L25 Chains: PB, T
Molecule details ›
Chains: PB, T
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
50S ribosomal protein L27 Chains: QB, U
Molecule details ›
Chains: QB, U
Length: 85 amino acids
Theoretical weight: 9.5 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60493 (Residues: 1-85; Coverage: 100%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
50S ribosomal protein L28 Chains: RB, V
Molecule details ›
Chains: RB, V
Length: 98 amino acids
Theoretical weight: 11.03 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: SB, W
Molecule details ›
Chains: SB, W
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: TB, X
Molecule details ›
Chains: TB, X
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L32 Chains: UB, Y
Molecule details ›
Chains: UB, Y
Length: 60 amino acids
Theoretical weight: 6.73 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: VB, Z
Molecule details ›
Chains: VB, Z
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P35871 (Residues: 1-54; Coverage: 100%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: AA, WB
Molecule details ›
Chains: AA, WB
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
50S ribosomal protein L35 Chains: BA, XB
Molecule details ›
Chains: BA, XB
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-65; Coverage: 100%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
30S ribosomal protein S2 Chains: CA, YB
Molecule details ›
Chains: CA, YB
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: DA, ZB
Molecule details ›
Chains: DA, ZB
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: AC, EA
Molecule details ›
Chains: AC, EA
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: BC, FA
Molecule details ›
Chains: BC, FA
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
30S ribosomal protein S6 Chains: CC, GA
Molecule details ›
Chains: CC, GA
Length: 101 amino acids
Theoretical weight: 11.99 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLP8 (Residues: 1-101; Coverage: 100%)
Gene names: TTHA0245, rpsF
Sequence domains: Ribosomal protein S6
30S ribosomal protein S7 Chains: DC, HA
Molecule details ›
Chains: DC, HA
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S ribosomal protein S8 Chains: EC, IA
Molecule details ›
Chains: EC, IA
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: A0A0M9AFS9 (Residues: 1-138; Coverage: 100%)
Gene names: BVI061214_01034, rpsH
Sequence domains: Ribosomal protein S8
30S ribosomal protein S9 Chains: FC, JA
Molecule details ›
Chains: FC, JA
Length: 128 amino acids
Theoretical weight: 14.43 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chains: GC, KA
Molecule details ›
Chains: GC, KA
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: HC, LA
Molecule details ›
Chains: HC, LA
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: IC, MA
Molecule details ›
Chains: IC, MA
Length: 132 amino acids
Theoretical weight: 14.64 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: JC, NA
Molecule details ›
Chains: JC, NA
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB27
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: KC, OA
Molecule details ›
Chains: KC, OA
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: A0A0N0BLP2 (Residues: 1-61; Coverage: 100%)
Gene names: BVI061214_01033, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
30S ribosomal protein S15 Chains: LC, PA
Molecule details ›
Chains: LC, PA
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: MC, QA
Molecule details ›
Chains: MC, QA
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: NC, RA
Molecule details ›
Chains: NC, RA
Length: 105 amino acids
Theoretical weight: 12.32 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: A0A0N0BLS5 (Residues: 1-105; Coverage: 100%)
Gene names: BVI061214_01029, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: OC, SA
Molecule details ›
Chains: OC, SA
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: PC, TA
Molecule details ›
Chains: PC, TA
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chains: QC, UA
Molecule details ›
Chains: QC, UA
Length: 106 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein Thx Chains: RC, VA
Molecule details ›
Chains: RC, VA
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
50S ribosomal protein L31 Chains: SC, TC
Molecule details ›
Chains: SC, TC
Length: 71 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-71; Coverage: 100%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
16S ribosomal RNA Chains: UC, YC
Molecule details ›
Chains: UC, YC
Length: 1509 nucleotides
Theoretical weight: 490 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chains: VC, ZC
Molecule details ›
Chains: VC, ZC
Length: 2893 nucleotides
Theoretical weight: 940.74 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: AD, WC
Molecule details ›
Chains: AD, WC
Length: 121 nucleotides
Theoretical weight: 39.21 KDa
Sequence domains: 5S ribosomal RNA
tRNA Chains: BD, ED, FD, XC
Molecule details ›
Chains: BD, ED, FD, XC
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
Messenger RNA Chains: GD, HD
Molecule details ›
Chains: GD, HD
Length: 27 nucleotides
Theoretical weight: 8.82 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 211.98Å b: 453.75Å c: 620.72Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.268 0.268 0.287