PDBe 4v7j

X-ray diffraction
3.3Å resolution

Structure of RelE nuclease bound to the 70S ribosome (precleavage state)

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 58-mer (preferred)
Entry contents:
52 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (58 distinct):
30S ribosomal protein S2 Chains: Ab, Bb
Molecule details ›
Chains: Ab, Bb
Length: 256 amino acids
Theoretical weight: 29.32 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80371 (Residues: 1-256; Coverage: 100%)
Gene names: TTHA0861, rps2, rpsB
Sequence domains: Ribosomal protein S2
30S ribosomal protein S3 Chains: Ac, Bc
Molecule details ›
Chains: Ac, Bc
Length: 239 amino acids
Theoretical weight: 26.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80372 (Residues: 1-239; Coverage: 100%)
Gene names: TTHA1686, rps3, rpsC
Sequence domains:
30S ribosomal protein S4 Chains: Ad, Bd
Molecule details ›
Chains: Ad, Bd
Length: 209 amino acids
Theoretical weight: 24.37 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80373 (Residues: 1-209; Coverage: 100%)
Gene names: TTHA1665, rps4, rpsD
Sequence domains:
30S ribosomal protein S5 Chains: Ae, Be
Molecule details ›
Chains: Ae, Be
Length: 162 amino acids
Theoretical weight: 17.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ5 (Residues: 1-162; Coverage: 100%)
Gene names: TTHA1675, rpsE
Sequence domains:
30S ribosomal protein S6 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
30S ribosomal protein S7 Chains: Ag, Bg
Molecule details ›
Chains: Ag, Bg
Length: 156 amino acids
Theoretical weight: 18.05 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P17291 (Residues: 1-156; Coverage: 100%)
Gene names: TTHA1696, rps7, rpsG
Sequence domains: Ribosomal protein S7p/S5e
30S ribosomal protein S8 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
30S ribosomal protein S9 Chains: Ai, Bi
Molecule details ›
Chains: Ai, Bi
Length: 128 amino acids
Theoretical weight: 14.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80374 (Residues: 1-128; Coverage: 100%)
Gene names: TTHA1464, rps9, rpsI
Sequence domains: Ribosomal protein S9/S16
30S ribosomal protein S10 Chains: Aj, Bj
Molecule details ›
Chains: Aj, Bj
Length: 105 amino acids
Theoretical weight: 11.95 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN7 (Residues: 1-105; Coverage: 100%)
Gene names: TTHA1693, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
30S ribosomal protein S11 Chains: Ak, Bk
Molecule details ›
Chains: Ak, Bk
Length: 129 amino acids
Theoretical weight: 13.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80376 (Residues: 1-129; Coverage: 100%)
Gene names: TTHA1666, rps11, rpsK
Sequence domains: Ribosomal protein S11
30S ribosomal protein S12 Chains: Al, Bl
Molecule details ›
Chains: Al, Bl
Length: 132 amino acids
Theoretical weight: 14.64 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN3 (Residues: 1-132; Coverage: 100%)
Gene names: TTHA1697, rpsL
Sequence domains: Ribosomal protein S12/S23
30S ribosomal protein S13 Chains: Am, Bm
Molecule details ›
Chains: Am, Bm
Length: 126 amino acids
Theoretical weight: 14.34 KDa
Source organism: Thermus thermophilus HB8
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: An, Bn
Molecule details ›
Chains: An, Bn
Length: 61 amino acids
Theoretical weight: 7.16 KDa
Source organism: Thermus thermophilus HB8
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: Ao, Bo
Molecule details ›
Chains: Ao, Bo
Length: 89 amino acids
Theoretical weight: 10.58 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJ76 (Residues: 1-89; Coverage: 100%)
Gene names: TTHA1138, rpsO
Sequence domains: Ribosomal protein S15
30S ribosomal protein S16 Chains: Ap, Bp
Molecule details ›
Chains: Ap, Bp
Length: 88 amino acids
Theoretical weight: 10.41 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SJH3 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA1035, rpsP
Sequence domains: Ribosomal protein S16
30S ribosomal protein S17 Chains: Aq, Bq
Molecule details ›
Chains: Aq, Bq
Length: 105 amino acids
Theoretical weight: 12.33 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0N0BLS5 (Residues: 1-105; Coverage: 100%)
Gene names: BVI061214_01029, rpsQ
Sequence domains: Ribosomal protein S17
30S ribosomal protein S18 Chains: Ar, Br
Molecule details ›
Chains: Ar, Br
Length: 88 amino acids
Theoretical weight: 10.26 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ0 (Residues: 1-88; Coverage: 100%)
Gene names: TTHA0243, rpsR
Sequence domains: Ribosomal protein S18
30S ribosomal protein S19 Chains: As, Bs
Molecule details ›
Chains: As, Bs
Length: 93 amino acids
Theoretical weight: 10.61 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP2 (Residues: 1-93; Coverage: 100%)
Gene names: TTHA1688, rpsS
Sequence domains: Ribosomal protein S19
30S ribosomal protein S20 Chains: At, Bt
Molecule details ›
Chains: At, Bt
Length: 106 amino acids
Theoretical weight: 11.74 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80380 (Residues: 1-106; Coverage: 100%)
Gene names: TTHA1397, rps20, rpsT
Sequence domains: Ribosomal protein S20
30S ribosomal protein Thx Chains: Au, Bu
Molecule details ›
Chains: Au, Bu
Length: 27 amino acids
Theoretical weight: 3.35 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SIH3 (Residues: 1-27; Coverage: 100%)
Gene names: TTHA1396, rpsU
Sequence domains: 30S ribosomal protein Thx
mRNA interferase toxin RelE Chains: Ay, By
Molecule details ›
Chains: Ay, By
Length: 95 amino acids
Theoretical weight: 11.07 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0C077 (Residues: 1-95; Coverage: 100%)
Gene names: JW1555, b1563, relE
Sequence domains: ParE toxin of type II toxin-antitoxin system, parDE
50S ribosomal protein L1 Chains: AC, BC
Molecule details ›
Chains: AC, BC
Length: 229 amino acids
Theoretical weight: 24.87 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLP7 (Residues: 1-229; Coverage: 100%)
Gene names: TTHA0246, rplA
Sequence domains: Ribosomal protein L1p/L10e family
50S ribosomal protein L2 Chains: AD, BD
Molecule details ›
Chains: AD, BD
Length: 276 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60405 (Residues: 1-276; Coverage: 100%)
Gene names: TTHA1689, rplB
Sequence domains:
50S ribosomal protein L3 Chains: AE, BE
Molecule details ›
Chains: AE, BE
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 Chains: AF, BF
Molecule details ›
Chains: AF, BF
Length: 210 amino acids
Theoretical weight: 23.27 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHN9 (Residues: 1-210; Coverage: 100%)
Gene names: TTHA1691, rplD
Sequence domains: Ribosomal protein L4/L1 family
50S ribosomal protein L5 Chains: AG, BG
Molecule details ›
Chains: AG, BG
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 Chains: AH, BH
Molecule details ›
Chains: AH, BH
Length: 180 amino acids
Theoretical weight: 19.57 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: A0A0M9ADP1 (Residues: 1-180; Coverage: 100%)
Gene names: BVI061214_01035, rplF
Sequence domains: Ribosomal protein L6
50S ribosomal protein L9 Chains: AI, BI
Molecule details ›
Chains: AI, BI
Length: 148 amino acids
Theoretical weight: 16.42 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SLQ1 (Residues: 1-148; Coverage: 100%)
Gene names: TTHA0242, rplI
Sequence domains:
50S ribosomal protein L10 Chains: AJ, BJ
Molecule details ›
Chains: AJ, BJ
Length: 173 amino acids
Theoretical weight: 18.59 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8VVE3 (Residues: 1-173; Coverage: 100%)
Gene names: TTHA0209, rplJ
Sequence domains: Ribosomal protein L10
50S ribosomal protein L13 Chains: AN, BN
Molecule details ›
Chains: AN, BN
Length: 140 amino acids
Theoretical weight: 15.93 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60488 (Residues: 1-140; Coverage: 100%)
Gene names: TTHA1465, rplM
Sequence domains: Ribosomal protein L13
50S ribosomal protein L14 Chains: AO, BO
Molecule details ›
Chains: AO, BO
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
50S ribosomal protein L15 Chains: AP, BP
Molecule details ›
Chains: AP, BP
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
50S ribosomal protein L16 Chains: AQ, BQ
Molecule details ›
Chains: AQ, BQ
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
50S ribosomal protein L17 Chains: AR, BR
Molecule details ›
Chains: AR, BR
Length: 118 amino acids
Theoretical weight: 13.75 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q9Z9H5 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA1663, rpl17, rplQ
Sequence domains: Ribosomal protein L17
50S ribosomal protein L18 Chains: AS, BS
Molecule details ›
Chains: AS, BS
Length: 112 amino acids
Theoretical weight: 12.64 KDa
Source organism: Thermus thermophilus HB8
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: AT, BT
Molecule details ›
Chains: AT, BT
Length: 146 amino acids
Theoretical weight: 17.19 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60490 (Residues: 1-146; Coverage: 100%)
Gene names: TTHA1031, rplS
Sequence domains: Ribosomal protein L19
50S ribosomal protein L20 Chains: AU, BU
Molecule details ›
Chains: AU, BU
Length: 118 amino acids
Theoretical weight: 13.78 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60491 (Residues: 1-118; Coverage: 100%)
Gene names: TTHA0553, rplT
Sequence domains: Ribosomal protein L20
50S ribosomal protein L21 Chains: AV, BV
Molecule details ›
Chains: AV, BV
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 Chains: AW, BW
Molecule details ›
Chains: AW, BW
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
50S ribosomal protein L23 Chains: AX, BX
Molecule details ›
Chains: AX, BX
Length: 96 amino acids
Theoretical weight: 10.76 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP0 (Residues: 1-96; Coverage: 100%)
Gene names: TTHA1690, rplW
Sequence domains: Ribosomal protein L23
50S ribosomal protein L24 Chains: AY, BY
Molecule details ›
Chains: AY, BY
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 Chains: AZ, BZ
Molecule details ›
Chains: AZ, BZ
Length: 206 amino acids
Theoretical weight: 23.24 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHZ1 (Residues: 1-206; Coverage: 100%)
Gene names: TTHA1589, rpl25, rplY, rptL5
Sequence domains:
50S ribosomal protein L27 Chains: A0, B0
Molecule details ›
Chains: A0, B0
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 L28 Chains: A1, B1
Molecule details ›
Chains: A1, B1
Length: 98 amino acids
Theoretical weight: 11 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P60494 (Residues: 1-98; Coverage: 100%)
Gene names: TTHA0042, rpmB
Sequence domains: Ribosomal L28 family
50S ribosomal protein L29 Chains: A2, B2
Molecule details ›
Chains: A2, B2
Length: 72 amino acids
Theoretical weight: 8.67 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHP6 (Residues: 1-72; Coverage: 100%)
Gene names: TTHA1684, rpmC
Sequence domains: Ribosomal L29 protein
50S ribosomal protein L30 Chains: A3, B3
Molecule details ›
Chains: A3, B3
Length: 60 amino acids
Theoretical weight: 6.8 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SHQ6 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA1674, rpmD
Sequence domains: Ribosomal protein L30p/L7e
50S ribosomal protein L31 Chains: A4, B4
Molecule details ›
Chains: A4, B4
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 Chains: A5, B5
Molecule details ›
Chains: A5, B5
Length: 60 amino acids
Theoretical weight: 6.72 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P80339 (Residues: 1-60; Coverage: 100%)
Gene names: TTHA0418, rpl32, rpmF
Sequence domains: Ribosomal L32p protein family
50S ribosomal protein L33 Chains: A6, B6
Molecule details ›
Chains: A6, B6
Length: 54 amino acids
Theoretical weight: 6.63 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: P35871 (Residues: 1-54; Coverage: 100%)
Gene names: TTHA0250, rpl33, rpmG
Sequence domains: Ribosomal protein L33
50S ribosomal protein L34 Chains: A7, B7
Molecule details ›
Chains: A7, B7
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: A8, B8
Molecule details ›
Chains: A8, B8
Length: 65 amino acids
Theoretical weight: 7.51 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKU1 (Residues: 1-65; Coverage: 100%)
Gene names: TTHA0552, rpmI
Sequence domains: Ribosomal protein L35
50S ribosomal protein L36 Chains: A9, B9
Molecule details ›
Chains: A9, B9
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
RNA (1504-MER) Chains: Aa, Ba
Molecule details ›
Chains: Aa, Ba
Length: 1504 nucleotides
Theoretical weight: 488.39 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
RNA (5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*A*AP*AP*AP*AP*UP*GP*(OMU)P*(A2M)P*(OMG)P*AP*AP*AP*A)-3') Chains: Ax, Bx
Molecule details ›
Chains: Ax, Bx
Length: 25 nucleotides
Theoretical weight: 8.26 KDa
RNA (77-MER) Chains: Av, Bv
Molecule details ›
Chains: Av, Bv
Length: 77 nucleotides
Theoretical weight: 24.82 KDa
Sequence domains: tRNA
RNA (77-MER) Chains: Aw, Bw
Molecule details ›
Chains: Aw, Bw
Length: 77 nucleotides
Theoretical weight: 24.8 KDa
Sequence domains: tRNA
RNA (2848-MER) Chains: AA, BA
Molecule details ›
Chains: AA, BA
Length: 2848 nucleotides
Theoretical weight: 926.37 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
RNA (119-MER) Chains: AB, BB
Molecule details ›
Chains: AB, BB
Length: 119 nucleotides
Theoretical weight: 38.55 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

2 bound ligands:

4 modified residues:

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 211.571Å b: 451.963Å c: 622.438Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.219 0.219 0.247
Expression system: Escherichia coli