PDBe 5a9z

Electron Microscopy
4.7Å resolution

Complex of Thermous thermophilus ribosome bound to BipA-GDPCP

Released:
Source organism: Thermus thermophilus HB8
Primary publication:
Structure of BipA in GTP form bound to the ratcheted ribosome.
Proc. Natl. Acad. Sci. U.S.A. (2015)
PMID: 26283392
Related structures: EMD-6396

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
Entry contents:
52 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (55 distinct):
BipA Chain: CA
Molecule details ›
Chain: CA
Length: 593 amino acids
Theoretical weight: 65.98 KDa
Source organism: Thermus thermophilus HB8
Unknown peptide Chain: Ag
Molecule details ›
Chain: Ag
Length: 128 amino acids
Theoretical weight: 10.91 KDa
Source organism: Thermus thermophilus HB8
30S ribosomal protein S2 Chain: BF
Molecule details ›
Chain: BF
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
30S ribosomal protein S3 Chain: BG
Molecule details ›
Chain: BG
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:
30S ribosomal protein S4 Chain: BH
Molecule details ›
Chain: BH
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:
30S ribosomal protein S5 Chain: BI
Molecule details ›
Chain: BI
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:
30S ribosomal protein S6 Chain: BJ
Molecule details ›
Chain: BJ
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
30S ribosomal protein S7 Chain: BK
Molecule details ›
Chain: BK
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
30S ribosomal protein S8 Chain: BL
Molecule details ›
Chain: BL
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
30S ribosomal protein S9 Chain: BM
Molecule details ›
Chain: BM
Length: 127 amino acids
Theoretical weight: 14.28 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
50S ribosomal protein L1 Chain: AC
Molecule details ›
Chain: AC
Length: 228 amino acids
Theoretical weight: 24.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 2-229; Coverage: 100%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
50S ribosomal protein L2 Chain: AD
Molecule details ›
Chain: AD
Length: 272 amino acids
Theoretical weight: 30.1 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 5-276; Coverage: 99%)
Gene names: TTHA1689, rplB
Sequence domains:
50S ribosomal protein L3 Chain: AE
Molecule details ›
Chain: AE
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
50S ribosomal protein L4 Chain: AF
Molecule details ›
Chain: AF
Length: 208 amino acids
Theoretical weight: 23.01 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 3-210; Coverage: 99%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chain: AG
Molecule details ›
Chain: AG
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 Chain: AH
Molecule details ›
Chain: AH
Length: 174 amino acids
Theoretical weight: 18.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY8 (Residues: 4-177; Coverage: 97%)
Gene names: TTHA1677, rplF
30S ribosomal protein S10 Chain: BN
Molecule details ›
Chain: BN
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
30S ribosomal protein S11 Chain: BO
Molecule details ›
Chain: BO
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
30S ribosomal protein S12 Chain: BP
Molecule details ›
Chain: BP
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
30S ribosomal protein S13 Chain: BQ
Molecule details ›
Chain: BQ
Length: 114 amino acids
Theoretical weight: 13.04 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 2-115; Coverage: 91%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
30S ribosomal protein S15 Chain: BS
Molecule details ›
Chain: BS
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
30S ribosomal protein S16 Chain: BT
Molecule details ›
Chain: BT
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 Chain: BU
Molecule details ›
Chain: BU
Length: 104 amino acids
Theoretical weight: 12.19 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLS5 (Residues: 2-105; Coverage: 99%)
Gene names: BVI061214_01029, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chain: BV
Molecule details ›
Chain: BV
Length: 73 amino acids
Theoretical weight: 8.48 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80382 (Residues: 16-88; Coverage: 83%)
Gene names: rps18, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chain: BW
Molecule details ›
Chain: BW
Length: 80 amino acids
Theoretical weight: 9.2 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 2-81; Coverage: 86%)
Gene names: TTHA1688, rpsS
30S ribosomal protein S20 Chain: BX
Molecule details ›
Chain: BX
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
30S ribosomal protein Thx Chain: BY
Molecule details ›
Chain: BY
Length: 24 amino acids
Theoretical weight: 2.96 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: F6DII0 (Residues: 2-25; Coverage: 89%)
Gene name: Ththe16_1406
50S ribosomal protein L10 Chain: AI
Molecule details ›
Chain: AI
Length: 153 amino acids
Theoretical weight: 16.43 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8VVE3 (Residues: 4-156; Coverage: 88%)
Gene names: TTHA0209, rplJ
50S ribosomal protein L11 Chain: AJ
Molecule details ›
Chain: AJ
Length: 134 amino acids
Theoretical weight: 14.17 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP6 (Residues: 4-137; Coverage: 91%)
Gene names: TTHA0247, rplK
Sequence domains: Ribosomal protein L11, N-terminal domain
50S ribosomal protein L13 Chain: AK
Molecule details ›
Chain: AK
Length: 139 amino acids
Theoretical weight: 15.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 2-140; Coverage: 99%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chain: AL
Molecule details ›
Chain: AL
Length: 122 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP8 (Residues: 1-122; Coverage: 100%)
Gene names: TTHA1682, rplN
Sequence domains: Ribosomal protein L14p/L23e
50S ribosomal protein L15 Chain: AM
Molecule details ›
Chain: AM
Length: 145 amino acids
Theoretical weight: 15.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ7 (Residues: 6-150; Coverage: 97%)
Gene names: TTHA1673, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
50S ribosomal protein L16 Chain: AN
Molecule details ›
Chain: AN
Length: 136 amino acids
Theoretical weight: 15.36 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60489 (Residues: 6-141; Coverage: 97%)
Gene names: TTHA1685, rplP
50S ribosomal protein L17 Chain: AO
Molecule details ›
Chain: AO
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
50S ribosomal protein L18 Chain: AP
Molecule details ›
Chain: AP
Length: 110 amino acids
Theoretical weight: 12.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 3-112; Coverage: 98%)
Gene names: TTHA1676, rplR
50S ribosomal protein L19 Chain: AQ
Molecule details ›
Chain: AQ
Length: 117 amino acids
Theoretical weight: 13.86 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-117; Coverage: 80%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chain: AR
Molecule details ›
Chain: AR
Length: 117 amino acids
Theoretical weight: 13.65 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 2-118; Coverage: 99%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chain: AS
Molecule details ›
Chain: AS
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
50S ribosomal protein L22 Chain: AT
Molecule details ›
Chain: AT
Length: 110 amino acids
Theoretical weight: 12.48 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP3 (Residues: 1-110; Coverage: 97%)
Gene names: TTHA1687, rplV
Sequence domains: Ribosomal protein L22p/L17e
50S ribosomal protein L23 Chain: AU
Molecule details ›
Chain: AU
Length: 94 amino acids
Theoretical weight: 10.5 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 3-96; Coverage: 98%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chain: AV
Molecule details ›
Chain: AV
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:
50S ribosomal protein L25 Chain: AW
Molecule details ›
Chain: AW
Length: 180 amino acids
Theoretical weight: 20.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-180; Coverage: 87%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
50S ribosomal protein L27 Chain: AX
Molecule details ›
Chain: AX
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
50S ribosomal protein L29 Chain: AY
Molecule details ›
Chain: AY
Length: 67 amino acids
Theoretical weight: 8.11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9LCY4 (Residues: 1-67; Coverage: 100%)
Gene names: rpl29, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chain: AZ
Molecule details ›
Chain: AZ
Length: 59 amino acids
Theoretical weight: 6.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 2-60; Coverage: 98%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chain: Aa
Molecule details ›
Chain: Aa
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
50S ribosomal protein L32 Chain: Ab
Molecule details ›
Chain: Ab
Length: 57 amino acids
Theoretical weight: 6.39 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 4-60; Coverage: 95%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chain: Ac
Molecule details ›
Chain: Ac
Length: 49 amino acids
Theoretical weight: 6.12 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 6-54; Coverage: 91%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chain: Ad
Molecule details ›
Chain: Ad
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 Chain: Ae
Molecule details ›
Chain: Ae
Length: 64 amino acids
Theoretical weight: 7.38 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-64; Coverage: 99%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chain: Af
Molecule details ›
Chain: Af
Length: 37 amino acids
Theoretical weight: 4.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHR2 (Residues: 1-37; Coverage: 100%)
Gene names: TTHA1668, rpmJ
Sequence domains: Ribosomal protein L36
30S ribosomal protein S14 type Z Chain: BR
Molecule details ›
Chain: BR
Length: 60 amino acids
Theoretical weight: 7.03 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLP2 (Residues: 2-61; Coverage: 98%)
Gene names: BVI061214_01033, rpsN, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
5S ribosomal RNA Chain: AB
Molecule details ›
Chain: AB
Length: 123 nucleotides
Theoretical weight: 39.85 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: BA
Molecule details ›
Chain: BA
Length: 1515 nucleotides
Theoretical weight: 491.78 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chain: AA
Molecule details ›
Chain: AA
Length: 2889 nucleotides
Theoretical weight: 939.57 KDa
Sequence domains: Bacterial large subunit ribosomal RNA

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.7Å
Relevant EMDB volumes: EMD-6396