4V9J

70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.86 Å
  • R-Value Free: 0.317
  • R-Value Work: 0.264

Literature

Macromolecules
Sequence Display for 4V9J

Classification: RIBOSOME / ANTIBIOTIC

Total Structure Weight: 4566591.00


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 AB, CB 235 Thermus thermophilus Gene Name(s): rpsB rps2 TT_C0509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 AC, CC 207 Thermus thermophilus Gene Name(s): rpsC rps3 TT_C1322
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 AD, CD 208 Thermus thermophilus Gene Name(s): rpsD rps4 TT_C1301
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 AE, CE 151 Thermus thermophilus Gene Name(s): rpsE rps5 TT_C1311
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 AF, CF 101 Thermus thermophilus Gene Name(s): rpsF rps6 TT_C1740
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 AG, CG 155 Thermus thermophilus Gene Name(s): rpsG rps7 TT_C1332
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 AH, CH 138 Thermus thermophilus Gene Name(s): rpsH rps8 TT_C1314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 AI, CI 127 Thermus thermophilus Gene Name(s): rpsI rps9 TT_C1100
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 AJ, CJ 99 Thermus thermophilus Gene Name(s): rpsJ rps10 TT_C1329
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 AK, CK 119 Thermus thermophilus Gene Name(s): rpsK rps11 TT_C1302
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 AL, CL 125 Thermus thermophilus Gene Name(s): rpsL rps12 TT_C1333
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 AM, CM 125 Thermus thermophilus Gene Name(s): rpsM rps13 TT_C1303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 type Z AN, CN 60 Thermus thermophilus Gene Name(s): rpsZ rps14 rpsN TT_C1315
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 AO, CO 88 Thermus thermophilus Gene Name(s): rpsO rps15 TT_C0773
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 AP, CP 84 Thermus thermophilus Gene Name(s): rpsP rps16 TT_C0673
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 AQ, CQ 100 Thermus thermophilus Gene Name(s): rpsQ rps17 TT_C1319
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 AR, CR 70 Thermus thermophilus Gene Name(s): rpsR rps18 TT_C1742
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 AS, CS 79 Thermus thermophilus Gene Name(s): rpsS rps19 TT_C1324
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 AT, CT 99 Thermus thermophilus Gene Name(s): rpsT rps20 TT_C1031
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Elongation factor G AY, CY 687 Thermus thermophilus Mutation: H129K, H226N
Gene Name(s): fusA TT_C1331
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Viomycin AU, CU 6 Streptomyces
50S ribosomal protein L1 BC, DC 228 Thermus thermophilus Mutation: I20V, H28R
Gene Name(s): rplA TT_C1739
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 BD, DD 275 Thermus thermophilus Gene Name(s): rplB TT_C1325
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 BE, DE 205 Thermus thermophilus Gene Name(s): rplC TT_C1328
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 BF, DF 208 Thermus thermophilus Gene Name(s): rplD TT_C1327
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 BG, DG 181 Thermus thermophilus Mutation: L5V
Gene Name(s): rplE TT_C1316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 BH, DH 167 Thermus thermophilus Gene Name(s): rplF TT_C1313
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10 BJ, DJ 170 Thermus thermophilus
50S ribosomal protein L11 BK, DK 140 Thermus thermophilus Gene Name(s): rplK TT_C1738
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 BO, DO 122 Thermus thermophilus Mutation: V69I
Gene Name(s): rplN TT_C1318
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 BP, DP 146 Thermus thermophilus Gene Name(s): rplO TT_C1309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 BQ, DQ 141 Thermus thermophilus Mutation: F32Y
Gene Name(s): rplP TT_C1321
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 BR, DR 117 Thermus thermophilus Gene Name(s): rplQ TT_C1299
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 BS, DS 99 Thermus thermophilus Gene Name(s): rplR TT_C1312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 BT, DT 138 Thermus thermophilus Mutation: K123Q, V135A
Gene Name(s): rplS TT_C0669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 BU, DU 117 Thermus thermophilus Gene Name(s): rplT TT_C0185
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 BV, DV 101 Thermus thermophilus Gene Name(s): rplU TT_C1424
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 BW, DW 113 Thermus thermophilus Gene Name(s): rplV TT_C1323
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 BX, DX 93 Thermus thermophilus Gene Name(s): rplW TT_C1326
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 BY, DY 107 Thermus thermophilus Gene Name(s): rplX TT_C1317
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 BZ, DZ 185 Thermus thermophilus Gene Name(s): rplY ctc TT_C1225
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 B0, D0 84 Thermus thermophilus Mutation: K11R
Gene Name(s): rpmA TT_C1423
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 B1, D1 93 Thermus thermophilus Mutation: R81K
Gene Name(s): rpmB TT_C1964
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 B4, D4 35 Thermus thermophilus Gene Name(s): rpmE TT_C0708
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 BN, DN 138 Thermus thermophilus Gene Name(s): rplM TT_C1101
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 B2, D2 71 Thermus thermophilus Gene Name(s): rpmC TT_C1320
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 B3, D3 60 Thermus thermophilus Gene Name(s): rpmD TT_C1310
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 B5, D5 59 Thermus thermophilus Mutation: I29T
Gene Name(s): rpmF rpl32 TT_C0050
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 B6, D6 50 Thermus thermophilus Gene Name(s): rpmG TT_C1735
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 B7, D7 49 Thermus thermophilus Gene Name(s): rpmH rpl34 TTHA0446
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 B8, D8 64 Thermus thermophilus Gene Name(s): rpmI TT_C0184
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 B9, D9 37 Thermus thermophilus Gene Name(s): rpmJ TT_C1304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7/L12 Be, De 103 Thermus thermophilus Gene Name(s): rplL TT_C1776
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7/L12 Bf, Bg, Df, Dg 31 Thermus thermophilus
50S ribosomal protein L7/L12 Bh, Dh 30 Thermus thermophilus
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA AA, CA 1511 Thermus thermophilus
messenger RNA AV, CV 18 Thermus thermophilus
tRNA-Met AW, CW 77 Escherichia coli
5S ribosomal RNA BB, DB 119 Thermus thermophilus
23S ribosomal RNA BA, DA 2879 Thermus thermophilus

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

AY, CY PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

AY, CY MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000226
Query on PRD_000226
AU, CU Viomycin Oligopeptide /
Antibiotic
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
BJ, Be, Bf, Bg, Bh, DJ, De, Df, Dg, Dh L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.86 Å
  • R-Value Free: 0.317
  • R-Value Work: 0.264
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 302.39 α = 90.00
b = 683.92 β = 90.00
c = 356.70 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2013-04-23
  • Released Date: 2014-07-09
  • Deposition author(s): Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.
  • Previous versions: 4KBT 4KBU 4KBV 4KBW

Revision History

  • 2014-12-10
    Type: Other
  • 2017-06-28
    Type: Database references