4V7J

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 4V7J

Classification: RIBOSOME

Total Structure Weight: 4532553.50


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 Ab, Bb 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 Ac, Bc 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 Ad, Bd 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 Ae, Be 162 Thermus thermophilus Gene Name(s): rpsE TTHA1675
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 Af, Bf 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 Ag, Bg 156 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 Ah, Bh 138 Thermus thermophilus Gene Name(s): rpsH BVI061214_01034
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 Ai, Bi 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 Aj, Bj 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 Ak, Bk 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 Al, Bl 132 Thermus thermophilus Gene Name(s): rpsL TTHA1697
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 Am, Bm 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 type Z An, Bn 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 Ao, Bo 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 Ap, Bp 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 Aq, Bq 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 Ar, Br 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 As, Bs 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 At, Bt 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein Thx Au, Bu 27 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Toxin relE Ay, By 95 Escherichia coli EC#: 3.1 IUBMB
Mutation: R45A, R81A
Gene Name(s): relE b1563 JW1555
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L1 AC, BC 229 Thermus thermophilus Gene Name(s): rplA TTHA0246
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 AD, BD 276 Thermus thermophilus Gene Name(s): rplB TTHA1689
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 AE, BE 206 Thermus thermophilus Gene Name(s): rplC TTHA1692
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 AF, BF 210 Thermus thermophilus Gene Name(s): rplD TTHA1691
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 AG, BG 182 Thermus thermophilus Gene Name(s): rplE TTHA1680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 AH, BH 180 Thermus thermophilus Gene Name(s): rplF BVI061214_01035
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 AI, BI 148 Thermus thermophilus Gene Name(s): rplI TTHA0242
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10 AJ, BJ 173 Thermus thermophilus Gene Name(s): rplJ TTHA0209
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 AN, BN 140 Thermus thermophilus Gene Name(s): rplM TTHA1465
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 AO, BO 122 Thermus thermophilus Gene Name(s): rplN TTHA1682
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 AP, BP 150 Thermus thermophilus Gene Name(s): rplO TTHA1673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 AQ, BQ 141 Thermus thermophilus Gene Name(s): rplP TTHA1685
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 AR, BR 118 Thermus thermophilus Gene Name(s): rplQ rpl17 TTHA1663
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 AS, BS 112 Thermus thermophilus Gene Name(s): rplR TTHA1676
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 AT, BT 146 Thermus thermophilus Gene Name(s): rplS TTHA1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 AU, BU 118 Thermus thermophilus Gene Name(s): rplT TTHA0553
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 AV, BV 101 Thermus thermophilus Gene Name(s): rplU TTHA1783
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 AW, BW 113 Thermus thermophilus Gene Name(s): rplV TTHA1687
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 AX, BX 96 Thermus thermophilus Gene Name(s): rplW TTHA1690
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 AY, BY 110 Thermus thermophilus Gene Name(s): rplX TTHA1681
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 AZ, BZ 206 Thermus thermophilus Gene Name(s): rplY rpl25 rptL5 TTHA1589
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 A0, B0 85 Thermus thermophilus Gene Name(s): rpmA TTHA1782
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 A1, B1 98 Thermus thermophilus Gene Name(s): rpmB TTHA0042
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 A2, B2 72 Thermus thermophilus Gene Name(s): rpmC TTHA1684
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 A3, B3 60 Thermus thermophilus Gene Name(s): rpmD TTHA1674
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 A4, B4 71 Thermus thermophilus Gene Name(s): rpmE TTHA1073
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 A5, B5 60 Thermus thermophilus Gene Name(s): rpmF rpl32 TTHA0418
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 A6, B6 54 Thermus thermophilus Gene Name(s): rpmG rpl33 TTHA0250
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 A7, B7 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 A8, B8 65 Thermus thermophilus Gene Name(s): rpmI TTHA0552
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 A9, B9 37 Thermus thermophilus Gene Name(s): rpmJ TTHA1668
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
RNA (1504-MER) Aa, Ba 1504 Thermus thermophilus
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') Ax, Bx 25 synthetic
RNA (77-MER) Av, Bv 77 Thermus thermophilus
RNA (77-MER) Aw, Bw 77 Thermus thermophilus
RNA (2848-MER) AA, BA 2848 Thermus thermophilus
RNA (119-MER) AB, BB 119 Thermus thermophilus

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A4, A9, Ad, An, B4, B9, Bd, Bn ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A1, A5, A7, AA, AB, AD, AF, AQ, AX, Aa, Am, Aq, Av, Aw, B0, B5, B7, BA, BB, BD, BF, BQ, BX, Ba, Bm, Bq, Bv, Bw, Bx MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 4 Unique
ID Chains Type Formula 2D Diagram Parent
OMU
Query on OMU
Ax, Bx RNA LINKING C10 H15 N2 O9 P U
A2M
Query on A2M
Ax, Bx RNA LINKING C11 H16 N5 O7 P A
OMG
Query on OMG
Ax, Bx RNA LINKING C11 H16 N5 O8 P G
5MU
Query on 5MU
Av, Bv RNA LINKING C10 H15 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.219
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 211.57 α = 90.00
b = 451.96 β = 90.00
c = 622.44 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2009-11-02
  • Released Date: 2014-07-09
  • Deposition author(s): Neubauer, C., Gao, Y.-G., Andersen, K.R., Dunham, C.M., Kelley, A.C., Hentschel, J., Gerdes, K., Ramakrishnan, V., Brodersen, D.E.
  • Previous versions: 3KIQ 3KIR 3KIS 3KIT

Revision History

  • Version 1_0: 2014-07-09

    Type: Initial release

  • Version 1_1: 2014-12-10

    Type: Other