4V6K

Structural insights into cognate vs. near-cognate discrimination during decoding.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.25 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 4V6K

Classification: RIBOSOME

Total Structure Weight: 2280365.00


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L1 AC 234 Escherichia coli Gene Name(s): rplA b3984 JW3947
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 AD 273 Escherichia coli Gene Name(s): rplB b3317 JW3279
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 AE 209 Escherichia coli Gene Name(s): rplC b3320 JW3282
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 AF 201 Escherichia coli Gene Name(s): rplD eryA b3319 JW3281
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 AG 179 Escherichia coli Gene Name(s): rplE b3308 JW3270
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 AH 177 Escherichia coli Gene Name(s): rplF b3305 JW3267
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 AI 149 Escherichia coli Gene Name(s): rplI b4203 JW4161
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 AJ 142 Escherichia coli Gene Name(s): rplK relC b3983 JW3946
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 AK 142 Escherichia coli Gene Name(s): rplM b3231 JW3200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 AL 123 Escherichia coli Gene Name(s): rplN b3310 JW3272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 AM 144 Escherichia coli Gene Name(s): rplO b3301 JW3263
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 AN 136 Escherichia coli Gene Name(s): rplP b3313 JW3275
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 AO 127 Escherichia coli Gene Name(s): rplQ b3294 JW3256
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 AP 117 Escherichia coli Gene Name(s): rplR b3304 JW3266
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 AQ 115 Escherichia coli Gene Name(s): rplS b2606 JW2587
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 AR 118 Escherichia coli Gene Name(s): rplT pdzA b1716 JW1706
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 AS 103 Escherichia coli Gene Name(s): rplU b3186 JW3153
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 AT 110 Escherichia coli Gene Name(s): rplV eryB b3315 JW3277
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 AU 100 Escherichia coli Gene Name(s): rplW b3318 JW3280
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 AV 104 Escherichia coli Gene Name(s): rplX b3309 JW3271
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 AW 94 Escherichia coli Gene Name(s): rplY b2185 JW2173
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 AX 85 Escherichia coli Gene Name(s): rpmA b3185 JW3152
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 AY 78 Escherichia coli Gene Name(s): rpmB b3637 JW3612
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 AZ 63 Escherichia coli Gene Name(s): rpmC b3312 JW3274
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 Aa 59 Escherichia coli Gene Name(s): rpmD b3302 JW3264
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 Ab 70 Escherichia coli Gene Name(s): rpmE b3936 JW3907
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 Ac 57 Escherichia coli Gene Name(s): rpmF b1089 JW1075
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 Ad 55 Escherichia coli Gene Name(s): rpmG b3636 JW3611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 Ae 46 Escherichia coli Gene Name(s): rpmH rimA ssaF b3703 JW3680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 Af 65 Escherichia coli Gene Name(s): rpmI b1717 JW1707
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 Ag 38 Escherichia coli
Elongation factor Tu 2 BC 393 Escherichia coli Gene Name(s): tufB b3980 JW3943
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S2 BF 241 Escherichia coli Gene Name(s): rpsB b0169 JW0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 BG 233 Escherichia coli Gene Name(s): rpsC b3314 JW3276
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 BH 206 Escherichia coli Gene Name(s): rpsD ramA b3296 JW3258
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 BI 167 Escherichia coli Gene Name(s): rpsE spc b3303 JW3265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 BJ 135 Escherichia coli Gene Name(s): rpsF b4200 JW4158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 BK 179 Escherichia coli Gene Name(s): rpsG b3341 JW3303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 BL 130 Escherichia coli Gene Name(s): rpsH b3306 JW3268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 BM 130 Escherichia coli Gene Name(s): rpsI b3230 JW3199
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 BN 103 Escherichia coli Gene Name(s): rpsJ nusE b3321 JW3283
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 BO 129 Escherichia coli Gene Name(s): rpsK b3297 JW3259
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 BP 124 Escherichia coli Gene Name(s): rpsL strA b3342 JW3304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 BQ 118 Escherichia coli Gene Name(s): rpsM b3298 JW3260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 BR 101 Escherichia coli Gene Name(s): rpsN b3307 JW3269
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 BS 89 Escherichia coli Gene Name(s): rpsO Z4526 ECs4046
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 BT 82 Escherichia coli Gene Name(s): rpsP b2609 JW2590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 BU 84 Escherichia coli Gene Name(s): rpsQ neaA b3311 JW3273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 BV 75 Escherichia coli Gene Name(s): rpsR b4202 JW4160
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 BW 92 Escherichia coli Gene Name(s): rpsS b3316 JW3278
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 BX 87 Escherichia coli Gene Name(s): rpsT b0023 JW0022
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S21 BY 71 Escherichia coli Gene Name(s): rpsU b3065 JW3037
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
ribosomal RNA 5S AA 120 Escherichia coli
ribosomal RNA 23S AB 2904 Escherichia coli
16S ribosomal RNA BA 1542 Escherichia coli
A/T-site tRNA Phe BB, BE 76 Escherichia coli
mRNA BD 24 Escherichia coli

Small Molecules
Modified Residues 20 Unique
ID Chains Type Formula 2D Diagram Parent
1MG
Query on 1MG
AB RNA LINKING C11 H16 N5 O8 P G
PSU
Query on PSU
AB, BA, BB, BE RNA LINKING C9 H13 N2 O9 P U
5MU
Query on 5MU
AB, BB, BE RNA LINKING C10 H15 N2 O9 P U
6MZ
Query on 6MZ
AB RNA LINKING C11 H16 N5 O7 P A
2MG
Query on 2MG
AB, BA RNA LINKING C11 H16 N5 O8 P G
3TD
Query on 3TD
AB RNA LINKING C10 H15 N2 O9 P U
5MC
Query on 5MC
AB, BA RNA LINKING C10 H16 N3 O8 P C
7MG
Query on 7MG
AB, BA, BB, BE RNA LINKING C11 H18 N5 O8 P G
OMG
Query on OMG
AB RNA LINKING C11 H16 N5 O8 P G
H2U
Query on H2U
AB, BB, BE RNA LINKING C9 H15 N2 O9 P U
OMC
Query on OMC
AB RNA LINKING C10 H16 N3 O8 P C
2MA
Query on 2MA
AB RNA LINKING C11 H16 N5 O7 P A
OMU
Query on OMU
AB RNA LINKING C10 H15 N2 O9 P U
CH
Query on CH
AB RNA LINKING C9 H15 N3 O8 P C
4OC
Query on 4OC
BA RNA LINKING C11 H18 N3 O8 P C
UR3
Query on UR3
BA RNA LINKING C10 H15 N2 O9 P U
MA6
Query on MA6
BA RNA LINKING C12 H18 N5 O7 P A
4SU
Query on 4SU
BB, BE RNA LINKING C9 H13 N2 O8 P S U
MIA
Query on MIA
BB, BE RNA LINKING C16 H26 N5 O7 P S A
3AU
Query on 3AU
BB, BE RNA linking C13 H20 N3 O11 P U

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.25 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2011-01-07
  • Released Date: 2014-07-09
  • Deposition author(s): Agirrezabala, X., Schreiner, E., Trabuco, L.G., Lei, J., Ortiz-Meoz, R.F., Schulten, K., Green, R., Frank, J.
  • Previous versions: 3IZU 3IZW

Revision History

  • Version 1_0: 2014-07-09

    Type: Initial release

  • Version 1_1: 2014-12-10

    Type: Other

  • Version 1_2: 2015-03-25

    Type: Other