4U25

Crystal structure of the E. coli ribosome bound to virginiamycin M1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.223

Literature

Macromolecules
Sequence Display for 4U25

Classification: RIBOSOME

Total Structure Weight: 4268914.50


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 AB, CB 218 Escherichia coli Gene Name(s): rpsB b0169 JW0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 AC, CC 206 Escherichia coli Gene Name(s): rpsC b3314 JW3276
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 AD, CD 205 Escherichia coli Gene Name(s): rpsD ramA b3296 JW3258
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 AE, CE 150 Escherichia coli Gene Name(s): rpsE spc b3303 JW3265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 AF, CF 100 Escherichia coli Gene Name(s): rpsF b4200 JW4158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 AG, CG 151 Escherichia coli Gene Name(s): rpsG b3341 JW3303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 AH, CH 129 Escherichia coli Gene Name(s): rpsH b3306 JW3268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 AI, CI 127 Escherichia coli Gene Name(s): rpsI b3230 JW3199
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 AJ, CJ 98 Escherichia coli Gene Name(s): rpsJ nusE b3321 JW3283
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 AK, CK 117 Escherichia coli Gene Name(s): rpsK b3297 JW3259
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 AL, CL 123 Escherichia coli Gene Name(s): rpsL strA b3342 JW3304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 AM, CM 114 Escherichia coli Gene Name(s): rpsM b3298 JW3260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 AN, CN 100 Escherichia coli Gene Name(s): rpsN b3307 JW3269
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 AO, CO 88 Escherichia coli Gene Name(s): rpsO secC b3165 JW3134
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 AP, CP 82 Escherichia coli Gene Name(s): rpsP b2609 JW2590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 AQ, CQ 80 Escherichia coli Gene Name(s): rpsQ neaA b3311 JW3273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 AR, CR 55 Escherichia coli Gene Name(s): rpsR b4202 JW4160
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 AS, CS 79 Escherichia coli Gene Name(s): rpsS b3316 JW3278
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 AT, CT 85 Escherichia coli Gene Name(s): rpsT b0023 JW0022
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S21 AU, CU 51 Escherichia coli Gene Name(s): rpsU b3065 JW3037
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 BC, DC 271 Escherichia coli Gene Name(s): rplB b3317 JW3279
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 BD, DD 209 Escherichia coli Gene Name(s): rplC b3320 JW3282
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 BE, DE 201 Escherichia coli Gene Name(s): rplD eryA b3319 JW3281
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 BF, DF 177 Escherichia coli Gene Name(s): rplE b3308 JW3270
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 BG, DG 176 Escherichia coli Gene Name(s): rplF b3305 JW3267
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 BH, DH 149 Escherichia coli Gene Name(s): rplI b4203 JW4161
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 BI, DI 141 Escherichia coli Gene Name(s): rplK relC b3983 JW3946
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 BJ, DJ 142 Escherichia coli Gene Name(s): rplM b3231 JW3200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 BK, DK 122 Escherichia coli Gene Name(s): rplN b3310 JW3272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 BL, DL 143 Escherichia coli Gene Name(s): rplO b3301 JW3263
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 BM, DM 136 Escherichia coli Gene Name(s): rplP b3313 JW3275
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 BN, DN 120 Escherichia coli Gene Name(s): rplQ b3294 JW3256
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 BO, DO 116 Escherichia coli Gene Name(s): rplR b3304 JW3266
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 BP, DP 114 Escherichia coli Gene Name(s): rplS b2606 JW2587
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 BQ, DQ 117 Escherichia coli Gene Name(s): rplT pdzA b1716 JW1706
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 BR, DR 103 Escherichia coli Gene Name(s): rplU b3186 JW3153
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 BS, DS 110 Escherichia coli Gene Name(s): rplV eryB b3315 JW3277
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 BT, DT 93 Escherichia coli Gene Name(s): rplW b3318 JW3280
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 BU, DU 102 Escherichia coli Gene Name(s): rplX b3309 JW3271
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 BV, DV 94 Escherichia coli Gene Name(s): rplY b2185 JW2173
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 BW, DW 76 Escherichia coli Gene Name(s): rpmA b3185 JW3152
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 BX, DX 77 Escherichia coli Gene Name(s): rpmB b3637 JW3612
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 BY, DY 63 Escherichia coli Gene Name(s): rpmC b3312 JW3274
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 BZ, DZ 58 Escherichia coli Gene Name(s): rpmD b3302 JW3264
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 B0, D0 56 Escherichia coli Gene Name(s): rpmF b1089 JW1075
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 B1, D1 50 Escherichia coli Gene Name(s): rpmG b3636 JW3611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 B2, D2 46 Escherichia coli Gene Name(s): rpmH rimA ssaF b3703 JW3680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 B3, D3 64 Escherichia coli Gene Name(s): rpmI b1717 JW1707
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 B4, D4 38 Escherichia coli Gene Name(s): rpmJ b3299 JW3261
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L1 B5 228 Thermus thermophilus Gene Name(s): rplA TTHA0246
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S rRNA AA, CA 1539 Escherichia coli
23S rRNA BA, DA 2903 Escherichia coli
5S rRNA BB, DB 119 Escherichia coli

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

BA, DA VIRGINIAMYCIN M1
C28 H35 N3 O7
DAIKHDNSXMZDCU-FQTGFAPKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

B4, D4 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

AA, AN, BA, BB, BD, BQ, CA, D2, DA, DB, DQ MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.223
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 210.64 α = 90.00
b = 434.61 β = 90.00
c = 625.01 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2014-07-16
  • Released Date: 2014-07-30
  • Deposition author(s): Noeske, J., Huang, J., Olivier, N.B., Giacobbe, R.A., Zambrowski, M., Cate, J.H.D.
  • Previous versions: 4TP4 4TP5 4TP6 4TP7

Revision History

  • 2014-10-01
    Type: Database references
  • 2014-12-10
    Type: Other