› 6gzz

Electron Microscopy
4.13Å resolution

T. thermophilus hibernating 100S ribosome (amc)

Released:
DOI: 10.2210/pdb6gzz/pdb
PDB entry 6gzz coloured by chain, front view.
PDB entry 6gzz coloured by chain, side view.
PDB entry 6gzz coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.
Flygaard RK, Boegholm N, Yusupov M, Jenner LB
Nat Commun 9 4179 (2018)
PMID: 30301898
Related structures: EMD-0105

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 108-mer (preferred)
PDBe Complex ID:
PDB-CPX-143897 (preferred)
Entry contents:
51 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (54 distinct):
Large ribosomal subunit protein uL2 Chains: C1, C2
Molecule details ›
Chains: C1, C2
Length: 272 amino acids
Theoretical weight: 29.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 2-273; Coverage: 99%)
Gene names: TTHA1689, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chains: D1, D2
Molecule details ›
Chains: D1, D2
Length: 205 amino acids
Theoretical weight: 22.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN8 (Residues: 1-205; Coverage: 100%)
Gene names: TTHA1692, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chains: E1, E2
Molecule details ›
Chains: E1, E2
Length: 208 amino acids
Theoretical weight: 23.07 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-208; Coverage: 99%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chains: F1, F2
Molecule details ›
Chains: F1, F2
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: G1, G2
Molecule details ›
Chains: G1, G2
Length: 170 amino acids
Theoretical weight: 18.57 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY8 (Residues: 2-171; Coverage: 94%)
Gene names: TTHA1677, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein bL9 Chains: H1, H2
Molecule details ›
Chains: H1, H2
Length: 50 amino acids
Theoretical weight: 5.45 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-50; Coverage: 34%)
Gene names: TTHA0242, rplI
Sequence domains: Ribosomal protein L9, N-terminal domain
Large ribosomal subunit protein uL13 Chains: I1, I2
Molecule details ›
Chains: I1, I2
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: J1, J2
Molecule details ›
Chains: J1, J2
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: K1, K2
Molecule details ›
Chains: K1, K2
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: L1, L2
Molecule details ›
Chains: L1, L2
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: M1, M2
Molecule details ›
Chains: M1, M2
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: N1, N2
Molecule details ›
Chains: N1, N2
Length: 111 amino acids
Theoretical weight: 12.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ4 (Residues: 2-112; Coverage: 99%)
Gene names: TTHA1676, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chains: O1, O2
Molecule details ›
Chains: O1, O2
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: P1, P2
Molecule details ›
Chains: P1, P2
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
Large ribosomal subunit protein bL21 Chains: Q1, Q2
Molecule details ›
Chains: Q1, Q2
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: R1, R2
Molecule details ›
Chains: R1, R2
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: S1, S2
Molecule details ›
Chains: S1, S2
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: T1, T2
Molecule details ›
Chains: T1, T2
Length: 102 amino acids
Theoretical weight: 11.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP9 (Residues: 2-103; Coverage: 93%)
Gene names: TTHA1681, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chains: U1, U2
Molecule details ›
Chains: U1, U2
Length: 179 amino acids
Theoretical weight: 20.27 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-179; Coverage: 87%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
Large ribosomal subunit protein bL27 Chains: V1, V2
Molecule details ›
Chains: V1, V2
Length: 77 amino acids
Theoretical weight: 8.7 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60493 (Residues: 9-85; Coverage: 91%)
Gene names: TTHA1782, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chains: W1, W2
Molecule details ›
Chains: W1, W2
Length: 97 amino acids
Theoretical weight: 10.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 2-98; Coverage: 99%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chains: X1, X2
Molecule details ›
Chains: X1, X2
Length: 69 amino acids
Theoretical weight: 8.3 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 4-72; Coverage: 96%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chains: Y1, Y2
Molecule details ›
Chains: Y1, Y2
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
Large ribosomal subunit protein bL31 Chains: Z1, Z2
Molecule details ›
Chains: Z1, Z2
Length: 63 amino acids
Theoretical weight: 7.38 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJE1 (Residues: 1-63; Coverage: 89%)
Gene names: TTHA1073, rpmE
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chains: a1, a2
Molecule details ›
Chains: a1, a2
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: b1, b2
Molecule details ›
Chains: b1, b2
Length: 45 amino acids
Theoretical weight: 5.6 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 9-53; Coverage: 83%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chains: c1, c2
Molecule details ›
Chains: c1, c2
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: d1, d2
Molecule details ›
Chains: d1, d2
Length: 61 amino acids
Theoretical weight: 6.99 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 2-62; Coverage: 94%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chains: e1, e2
Molecule details ›
Chains: e1, e2
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
Small ribosomal subunit protein uS2 Chains: B3, B4
Molecule details ›
Chains: B3, B4
Length: 237 amino acids
Theoretical weight: 27.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 4-240; Coverage: 93%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chains: C3, C4
Molecule details ›
Chains: C3, C4
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:
Small ribosomal subunit protein uS4 Chains: D3, D4
Molecule details ›
Chains: D3, D4
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: E3, E4
Molecule details ›
Chains: E3, E4
Length: 151 amino acids
Theoretical weight: 16.46 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 5-155; Coverage: 93%)
Gene names: TTHA1675, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chains: F3, F4
Molecule details ›
Chains: F3, F4
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: G3, G4
Molecule details ›
Chains: G3, G4
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: H3, H4
Molecule details ›
Chains: H3, H4
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: I3, I4
Molecule details ›
Chains: I3, I4
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
Small ribosomal subunit protein uS10 Chains: J3, J4
Molecule details ›
Chains: J3, J4
Length: 99 amino acids
Theoretical weight: 11.4 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 3-101; Coverage: 94%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chains: K3, K4
Molecule details ›
Chains: K3, K4
Length: 118 amino acids
Theoretical weight: 12.52 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 11-128; Coverage: 92%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chains: L3, L4
Molecule details ›
Chains: L3, L4
Length: 125 amino acids
Theoretical weight: 13.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 2-126; Coverage: 95%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chains: M3, M4
Molecule details ›
Chains: M3, M4
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80377 (Residues: 2-118; Coverage: 93%)
Gene names: TTHA1667, rps13, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14 Chains: N3, N4
Molecule details ›
Chains: N3, N4
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: O3, O4
Molecule details ›
Chains: O3, O4
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: P3, P4
Molecule details ›
Chains: P3, P4
Length: 84 amino acids
Theoretical weight: 10 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-84; Coverage: 96%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chains: Q3, Q4
Molecule details ›
Chains: Q3, Q4
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P0DOY7 (Residues: 2-101; Coverage: 95%)
Gene names: TTHA1683, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chains: R3, R4
Molecule details ›
Chains: R3, R4
Length: 62 amino acids
Theoretical weight: 7.31 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 27-88; Coverage: 71%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chains: S3, S4
Molecule details ›
Chains: S3, S4
Length: 78 amino acids
Theoretical weight: 8.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 7-84; Coverage: 84%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chains: T3, T4
Molecule details ›
Chains: T3, T4
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: U3, U4
Molecule details ›
Chains: U3, U4
Length: 25 amino acids
Theoretical weight: 3.09 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 2-26; Coverage: 93%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
Ribosome hibernation promoting factor Chains: W4, X3
Molecule details ›
Chains: W4, X3
Length: 57 amino acids
Theoretical weight: 6.77 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SIS0 (Residues: 129-185; Coverage: 31%)
Gene names: TTHA1294, hpf
Sequence domains: Sigma 54 modulation/S30EA ribosomal protein C terminus
Ribosome hibernation promoting factor Chains: V3, V4
Molecule details ›
Chains: V3, V4
Length: 119 amino acids
Theoretical weight: 13.69 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SIS0 (Residues: 2-120; Coverage: 64%)
Gene names: TTHA1294, hpf
Sequence domains: Sigma 54 modulation protein / S30EA ribosomal protein
23S ribosomal RNA Chains: A1, A2
Molecule details ›
Chains: A1, A2
Length: 2912 nucleotides
Theoretical weight: 947.01 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chains: B1, B2
Molecule details ›
Chains: B1, B2
Length: 122 nucleotides
Theoretical weight: 39.54 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chains: A3, A4
Molecule details ›
Chains: A3, A4
Length: 1506 nucleotides
Theoretical weight: 489 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.13Å
Relevant EMDB volumes: EMD-0105
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Ribosomal Hibernation-Associated Factors in Escherichia coli.
Maki et al. (2021)
6 more