4wt8

X-ray diffraction
3.4Å resolution

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

Released:

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero 58-mer
hetero 59-mer (preferred)
PDBe Complex ID:
PDB-CPX-219269 (preferred)
Entry contents:
54 distinct polypeptide molecules
10 distinct RNA molecules
Macromolecules (64 distinct):
Small ribosomal subunit protein uS2 Chains: AA, BA
Molecule details ›
Chains: AA, BA
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 Chain: AC
Molecule details ›
Chain: AC
Length: 238 amino acids
Theoretical weight: 26.62 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-238; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chains: AD, BD
Molecule details ›
Chains: AD, BD
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, BE
Molecule details ›
Chains: AE, BE
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, BF
Molecule details ›
Chains: AF, BF
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, BG
Molecule details ›
Chains: AG, BG
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
Small ribosomal subunit protein uS8 Chains: AH, BH
Molecule details ›
Chains: AH, BH
Length: 138 amino acids
Theoretical weight: 15.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY9 (Residues: 1-138; Coverage: 100%)
Gene names: TTHA1678, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chains: AI, BI
Molecule details ›
Chains: AI, BI
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, BJ
Molecule details ›
Chains: AJ, BJ
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, BK
Molecule details ›
Chains: AK, BK
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, BL
Molecule details ›
Chains: AL, BL
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, BM
Molecule details ›
Chains: AM, BM
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
Small ribosomal subunit protein uS14 Chains: AN, BN
Molecule details ›
Chains: AN, BN
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY6 (Residues: 2-61; Coverage: 98%)
Gene names: TTHA1679, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chains: AO, BO
Molecule details ›
Chains: AO, BO
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, BP
Molecule details ›
Chains: AP, BP
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
Small ribosomal subunit protein uS17 Chains: AR, BR
Molecule details ›
Chains: AR, BR
Length: 99 amino acids
Theoretical weight: 11.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 2-100; Coverage: 94%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: AS, BS
Molecule details ›
Chains: AS, BS
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: AT, BT
Molecule details ›
Chains: AT, BT
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: AU, BU
Molecule details ›
Chains: AU, BU
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: AW, BW
Molecule details ›
Chains: AW, BW
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
Small ribosomal subunit protein uS3 Chain: BC
Molecule details ›
Chain: BC
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:
Large ribosomal subunit protein uL1 Chain: CA
Molecule details ›
Chain: CA
Length: 206 amino acids
Theoretical weight: 19.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 19-111; Coverage: 41%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL2 Chains: CB, DB
Molecule details ›
Chains: CB, DB
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: CC, DC
Molecule details ›
Chains: CC, DC
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: CD, DD
Molecule details ›
Chains: CD, DD
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: CE, DE
Molecule details ›
Chains: CE, DE
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:
Large ribosomal subunit protein uL6 Chains: CF, DF
Molecule details ›
Chains: CF, DF
Length: 159 amino acids
Theoretical weight: 17.36 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY8 (Residues: 12-170; Coverage: 88%)
Gene names: TTHA1677, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chains: CI, DI
Molecule details ›
Chains: CI, 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:
ribosomal L10 protein Chains: CJ, DJ
Molecule details ›
Chains: CJ, DJ
Length: 130 amino acids
Theoretical weight: 11.08 KDa
Source organism: Thermus thermophilus HB8
Large ribosomal subunit protein uL13 Chains: CM, DM
Molecule details ›
Chains: CM, DM
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: CN, DN
Molecule details ›
Chains: CN, DN
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: CO, DO
Molecule details ›
Chains: CO, DO
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: CP, DP
Molecule details ›
Chains: CP, DP
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: CQ, DQ
Molecule details ›
Chains: CQ, DQ
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: CR, DR
Molecule details ›
Chains: CR, DR
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: CS, DS
Molecule details ›
Chains: CS, DS
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: CT, DT
Molecule details ›
Chains: CT, DT
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: CU, DU
Molecule details ›
Chains: CU, DU
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 Chain: CW
Molecule details ›
Chain: CW
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: CX, DX
Molecule details ›
Chains: CX, 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: CY, DY
Molecule details ›
Chains: CY, 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: CZ, DZ
Molecule details ›
Chains: CZ, 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: Ca, Da
Molecule details ›
Chains: Ca, Da
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: CH, DH
Molecule details ›
Chains: CH, DH
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: CK, DK
Molecule details ›
Chains: CK, DK
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: CL, DL
Molecule details ›
Chains: CL, DL
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: C5, D5
Molecule details ›
Chains: C5, D5
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: C6, D6
Molecule details ›
Chains: C6, D6
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: C7, D7
Molecule details ›
Chains: C7, D7
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: C8, D8
Molecule details ›
Chains: C8, D8
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: C9, D9
Molecule details ›
Chains: C9, D9
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: C0, D0
Molecule details ›
Chains: C0, D0
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
Large ribosomal subunit protein uL1 Chain: DA
Molecule details ›
Chain: DA
Length: 206 amino acids
Theoretical weight: 19.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 19-111; Coverage: 41%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL22 Chain: DW
Molecule details ›
Chain: DW
Length: 113 amino acids
Theoretical weight: 12.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-112; Coverage: 99%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
Messenger RNA Chain: A2
Molecule details ›
Chain: A2
Length: 9 nucleotides
Theoretical weight: 2.84 KDa
RNA (1504-MER) Chains: Ab, Bb
Molecule details ›
Chains: Ab, Bb
Length: 1504 nucleotides
Theoretical weight: 488.39 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
Messenger RNA Chain: B2
Molecule details ›
Chain: B2
Length: 10 nucleotides
Theoretical weight: 3.17 KDa
A site tNA, E site tNA Chains: C2, C3, D3
Molecule details ›
Chains: C2, C3, D3
Length: 76 nucleotides
Theoretical weight: 24.49 KDa
Sequence domains: tRNA
P site trNA Chain: C4
Molecule details ›
Chain: C4
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
23S ribosomal RNA Chains: C1, D1
Molecule details ›
Chains: C1, D1
Length: 2899 nucleotides
Theoretical weight: 942.98 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: Cs, Ds
Molecule details ›
Chains: Cs, Ds
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA
tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3') Chain: D2
Molecule details ›
Chain: D2
Length: 20 nucleotides
Theoretical weight: 6.29 KDa
tRNA (76-MER) Chain: D4
Molecule details ›
Chain: D4
Length: 76 nucleotides
Theoretical weight: 24.5 KDa
Sequence domains: tRNA
DNA (55-MER) Chain: DV
Molecule details ›
Chain: DV
Length: 55 nucleotides
Theoretical weight: 17.82 KDa
Sequence domains: tRNA

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 214.21Å b: 457.45Å c: 639.66Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.241