5LZE

Structure of the 70S ribosome with Sec-tRNASec in the classical pre-translocation state (C)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 5LZE

Classification: RIBOSOME

Total Structure Weight: 2198966.50


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 b 218 Escherichia coli Gene Name(s): rpsB b0169 JW0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 c 206 Escherichia coli Gene Name(s): rpsC b3314 JW3276
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 d 205 Escherichia coli Gene Name(s): rpsD ramA b3296 JW3258
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 e 157 Escherichia coli Gene Name(s): rpsE spc b3303 JW3265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 f 100 Escherichia coli Gene Name(s): rpsF b4200 JW4158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 g 151 Escherichia coli Gene Name(s): rpsG b3341 JW3303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 h 129 Escherichia coli Gene Name(s): rpsH b3306 JW3268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 i 127 Escherichia coli Gene Name(s): rpsI b3230 JW3199
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 j 98 Escherichia coli Gene Name(s): rpsJ nusE b3321 JW3283
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 k 116 Escherichia coli Gene Name(s): rpsK b3297 JW3259
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 l 123 Escherichia coli Gene Name(s): rpsL strA b3342 JW3304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 m 114 Escherichia coli Gene Name(s): rpsM b3298 JW3260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 n 100 Escherichia coli Gene Name(s): rpsN b3307 JW3269
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 o 88 Escherichia coli Gene Name(s): rpsO secC b3165 JW3134
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 p 82 Escherichia coli Gene Name(s): rpsP b2609 JW2590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 q 80 Escherichia coli Gene Name(s): rpsQ neaA b3311 JW3273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 r 65 Escherichia coli Gene Name(s): rpsR b4202 JW4160
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 s 79 Escherichia coli Gene Name(s): rpsS b3316 JW3278
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 t 85 Escherichia coli Gene Name(s): rpsT b0023 JW0022
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S21 u 65 Escherichia coli Gene Name(s): rpsU b3065 JW3037
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L2 C 271 Escherichia coli Gene Name(s): rplB b3317 JW3279
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 D 209 Escherichia coli Gene Name(s): rplC b3320 JW3282
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 E 201 Escherichia coli Gene Name(s): rplD eryA b3319 JW3281
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 F 177 Escherichia coli Gene Name(s): rplE b3308 JW3270
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 G 176 Escherichia coli Gene Name(s): rplF b3305 JW3267
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L11 I 141 Escherichia coli Gene Name(s): rplK relC b3983 JW3946
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L9 H 149 Escherichia coli Gene Name(s): rplI b4203 JW4161
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 J 142 Escherichia coli Gene Name(s): rplM b3231 JW3200
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 K 122 Escherichia coli Gene Name(s): rplN b3310 JW3272
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 L 143 Escherichia coli Gene Name(s): rplO b3301 JW3263
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 M 136 Escherichia coli Gene Name(s): rplP b3313 JW3275
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 N 120 Escherichia coli Gene Name(s): rplQ b3294 JW3256
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 O 116 Escherichia coli Gene Name(s): rplR b3304 JW3266
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 P 114 Escherichia coli Gene Name(s): rplS b2606 JW2587
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 Q 117 Escherichia coli Gene Name(s): rplT pdzA b1716 JW1706
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 R 103 Escherichia coli Gene Name(s): rplU b3186 JW3153
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 S 110 Escherichia coli Gene Name(s): rplV eryB b3315 JW3277
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 T 93 Escherichia coli Gene Name(s): rplW b3318 JW3280
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 U 102 Escherichia coli Gene Name(s): rplX b3309 JW3271
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 V 94 Escherichia coli Gene Name(s): rplY b2185 JW2173
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 W 75 Escherichia coli Gene Name(s): rpmA b3185 JW3152
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L28 X 77 Escherichia coli Gene Name(s): rpmB b3637 JW3612
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 Y 63 Escherichia coli Gene Name(s): rpmC b3312 JW3274
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 Z 58 Escherichia coli Gene Name(s): rpmD b3302 JW3264
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 0 56 Escherichia coli Gene Name(s): rpmF b1089 JW1075
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L33 1 50 Escherichia coli Gene Name(s): rpmG b3636 JW3611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 2 46 Escherichia coli Gene Name(s): rpmH rimA ssaF b3703 JW3680
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 3 64 Escherichia coli Gene Name(s): rpmI b1717 JW1707
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 4 38 Escherichia coli Gene Name(s): rpmJ b3299 JW3261
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31 6 66 Escherichia coli Gene Name(s): rpmE b3936 JW3907
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA a 1539 Escherichia coli
tRNAfMet v 77 Escherichia coli
SECIS mRNA x 48 Escherichia coli
fMetSec-tRNASec y 95 Escherichia coli
23S ribosomal RNA A 2903 Escherichia coli
5S ribosomal RNA B 120 Escherichia coli
CCA 3' end of E-site tRNASec (low occupancy) w 3 Escherichia coli

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

4, 6 ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 18 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
A, a, v, y RNA LINKING C9 H13 N2 O9 P U
G7M
Query on G7M
A, a RNA LINKING C11 H17 N5 O8 P G
2MG
Query on 2MG
A, a RNA LINKING C11 H16 N5 O8 P G
5MC
Query on 5MC
A, a RNA LINKING C10 H16 N3 O8 P C
4OC
Query on 4OC
a RNA LINKING C11 H18 N3 O8 P C
UR3
Query on UR3
a RNA LINKING C10 H15 N2 O9 P U
MA6
Query on MA6
a RNA LINKING C12 H18 N5 O7 P A
4SU
Query on 4SU
v RNA LINKING C9 H13 N2 O8 P S U
H2U
Query on H2U
A, v, y RNA LINKING C9 H15 N2 O9 P U
5MU
Query on 5MU
A, v, y RNA LINKING C10 H15 N2 O9 P U
6IA
Query on 6IA
y RNA LINKING C15 H24 N5 O7 P A
1MG
Query on 1MG
A RNA LINKING C11 H16 N5 O8 P G
6MZ
Query on 6MZ
A RNA LINKING C11 H16 N5 O7 P A
3TD
Query on 3TD
A RNA LINKING C10 H15 N2 O9 P U
OMG
Query on OMG
A RNA LINKING C11 H16 N5 O8 P G
OMC
Query on OMC
A RNA LINKING C10 H16 N3 O8 P C
2MA
Query on 2MA
A RNA LINKING C11 H16 N5 O7 P A
OMU
Query on OMU
A RNA LINKING C10 H15 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2016-09-29
  • Released Date: 2016-11-23
  • Deposition author(s): Fischer, N., Neumann, P., Bock, L.V., Maracci, C., Wang, Z., Paleskava, A., Konevega, A.L., Schroeder, G.F., Grubmueller, H., Ficner, R., Rodnina, M.V., Stark, H.

Revision History

  • Version 1_0: 2016-11-23

    Type: Initial release

  • Version 1_1: 2016-11-30

    Type: Database references

  • Version 1_2: 2016-12-14

    Type: Database references

  • Version 1_3: 2017-08-30

    Type: Author supporting evidence, Data collection, Derived calculations, Refinement description