4V6T

Structure of the bacterial ribosome complexed by tmRNA-SmpB and EF-G during translocation and MLD-loading

Structural Biology Knowledgebase: 4V6T SBKB.org


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.3 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice (cryo Em)
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 4V6T

Classification: RIBOSOME

Total Structure Weight: 2348613.00


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 AB 218 Escherichia coli Gene Name(s): rpsB b0169 JW0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 AC 206 Escherichia coli Gene Name(s): rpsC b3314 JW3276
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 AD 205 Escherichia coli Gene Name(s): rpsD ramA b3296 JW3258
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 AE 150 Escherichia coli Gene Name(s): rpsE spc b3303 JW3265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 AF 100 Escherichia coli Gene Name(s): rpsF b4200 JW4158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 AG 151 Escherichia coli Gene Name(s): rpsG b3341 JW3303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 AH 129 Escherichia coli Gene Name(s): rpsH b3306 JW3268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 AI 127 Escherichia coli Gene Name(s): rpsI b3230 JW3199
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 AJ 98 Escherichia coli Gene Name(s): rpsJ nusE b3321 JW3283
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 AK 117 Escherichia coli Gene Name(s): rpsK b3297 JW3259
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 AL 123 Escherichia coli Gene Name(s): rpsL strA b3342 JW3304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 AM 114 Escherichia coli Gene Name(s): rpsM b3298 JW3260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 AN 100 Escherichia coli Gene Name(s): rpsN b3307 JW3269
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 AO 88 Escherichia coli Gene Name(s): rpsO secC b3165 JW3134
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 AP 82 Escherichia coli Gene Name(s): rpsP b2609 JW2590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 AQ 80 Escherichia coli Gene Name(s): rpsQ neaA b3311 JW3273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 AR 55 Escherichia coli Gene Name(s): rpsR b4202 JW4160
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 AS 79 Escherichia coli Gene Name(s): rpsS b3316 JW3278
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 AT 85 Escherichia coli Gene Name(s): rpsT b0023 JW0022
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S21 AU 51 Escherichia coli Gene Name(s): rpsU b3065 JW3037
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SsrA-binding protein AW 123 Escherichia coli Fragment: SEE REMARK 999
elongation factor G AY 691 Escherichia coli Fragment: SEE REMARK 999
50S ribosomal protein L2 BC 271 Escherichia coli Gene Name(s): rplB b3317 JW3279
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 BD 209 Escherichia coli Gene Name(s): rplC b3320 JW3282
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 BE 201 Escherichia coli Gene Name(s): rplD eryA b3319 JW3281
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 BF 177 Escherichia coli Gene Name(s): rplE b3308 JW3270
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 BG 176 Escherichia coli Gene Name(s): rplF b3305 JW3267
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 BH 149 Escherichia coli Gene Name(s): rplI b4203 JW4161
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 BI 141 Escherichia coli Gene Name(s): rplK relC b3983 JW3946
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 BJ 142 Escherichia coli Gene Name(s): rplM b3231 JW3200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 BK 122 Escherichia coli Gene Name(s): rplN b3310 JW3272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 BL 143 Escherichia coli Gene Name(s): rplO b3301 JW3263
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 BM 136 Escherichia coli Gene Name(s): rplP b3313 JW3275
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 BN 120 Escherichia coli Gene Name(s): rplQ b3294 JW3256
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 BO 116 Escherichia coli Gene Name(s): rplR b3304 JW3266
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 BP 114 Escherichia coli Gene Name(s): rplS b2606 JW2587
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 BQ 117 Escherichia coli Gene Name(s): rplT pdzA b1716 JW1706
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 BR 103 Escherichia coli Gene Name(s): rplU b3186 JW3153
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 BS 110 Escherichia coli Gene Name(s): rplV eryB b3315 JW3277
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 BT 93 Escherichia coli Gene Name(s): rplW b3318 JW3280
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 BU 102 Escherichia coli Gene Name(s): rplX b3309 JW3271
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 BV 94 Escherichia coli Gene Name(s): rplY b2185 JW2173
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 BW 76 Escherichia coli Gene Name(s): rpmA b3185 JW3152
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 BX 77 Escherichia coli Gene Name(s): rpmB b3637 JW3612
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 BY 63 Escherichia coli Gene Name(s): rpmC b3312 JW3274
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 BZ 58 Escherichia coli Gene Name(s): rpmD b3302 JW3264
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 B0 56 Escherichia coli Gene Name(s): rpmF b1089 JW1075
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 B1 50 Escherichia coli Gene Name(s): rpmG b3636 JW3611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 B2 46 Escherichia coli Gene Name(s): rpmH rimA ssaF b3703 JW3680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 B3 64 Escherichia coli Gene Name(s): rpmI b1717 JW1707
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 B4 38 Escherichia coli Gene Name(s): rpmJ b3299 JW3261
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA AA 1539 Escherichia coli
full length transfer messenger RNA (tmRNA) AV 363 Escherichia coli
formyl-methionine specific initiator transfer RNA AX 77 Escherichia coli
23S ribosomal RNA BA 2903 Escherichia coli
5S ribosomal RNA BB 119 Escherichia coli

Small Molecules
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5MU
Query on 5MU
AV RNA LINKING C10 H15 N2 O9 P U
PSU
Query on PSU
AV RNA LINKING C9 H13 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.3 Å
  • Aggregation State: Particle
  • Specimen Type: Vitreous Ice (cryo Em)
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2012-01-27
  • Released Date: 2014-07-09
  • Deposition author(s): Ramrath, D.J.F., Yamamoto, H., Rother, K., Wittek, D., Pech, M., Mielke, T., Loerke, J., Scheerer, P., Ivanov, P., Teraoka, Y., Shpanchenko, O., Nierhaus, K.H., Spahn, C.M.T.
  • Previous versions: 3J18 3J19

Revision History

  • 2015-04-01
    Type: Other | Details: Remove NDB ID
  • 2014-12-10
    Type: Other | Details: Move to main ftp archive