5ME0

Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 5ME0

Classification: RIBOSOME

Total Structure Weight: 953587.69


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 B 241 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsB b0169 JW0164
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S3 C 233 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsC b3314 JW3276
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S4 D 206 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsD ramA b3296 JW3258
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S5 E 167 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsE spc b3303 JW3265
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S6 F 131 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsF b4200 JW4158
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S7 G 156 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsG b3341 JW3303
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S8 H 130 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsH b3306 JW3268
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S9 I 130 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsI b3230 JW3199
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S10 J 103 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsJ nusE b3321 JW3283
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S11 K 129 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsK b3297 JW3259
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S12 L 123 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsL strA b3342 JW3304
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S13 M 118 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsM b3298 JW3260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S14 N 101 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsN b3307 JW3269
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S15 O 89 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsO secC b3165 JW3134
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S16 P 102 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsP ACN002_2645 HMPREF3040_04031 HMPREF3041_00235
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S17 Q 84 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsQ neaA b3311 JW3273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S18 R 75 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsR b4202 JW4160
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S19 S 92 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsS b3316 JW3278
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S20 T 87 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsT b0023 JW0022
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
30S ribosomal protein S21 U 71 Escherichia coli Details: Taken from PDB entry 4YBB
Gene Name(s): rpsU b3065 JW3037
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Translation initiation factor IF-1 V 72 Thermus thermophilus Details: Taken from PDB entry 1HR0
Gene Name(s): infA TTHA1669
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Translation initiation factor IF-2 W 890 Escherichia coli Details: Taken from PDB entry 3JCN
Gene Name(s): infB gicD ssyG b3168 JW3137
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Translation initiation factor IF-3 Y 171 Geobacillus stearothermophilus Details: Taken from PDB entry 1TIF
Gene Name(s): infC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Translation initiation factor IF-3 Z 144 Escherichia coli Details: Taken from PDB entry 2IFE
Gene Name(s): infC fit srjA b1718 JW5829
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA A 1534 Escherichia coli Taken from PDB entry 4YBB
fMet-tRNA X 77 Escherichia coli Taken from PDB entry 3JCN

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

X N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 11 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
A, X RNA LINKING C9 H13 N2 O9 P U
G7M
Query on G7M
A RNA LINKING C11 H17 N5 O8 P G
2MG
Query on 2MG
A RNA LINKING C11 H16 N5 O8 P G
5MC
Query on 5MC
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
D2T
Query on D2T
L L-peptide linking C5 H9 N O4 S ASP
4SU
Query on 4SU
X RNA LINKING C9 H13 N2 O8 P S U
H2U
Query on H2U
X RNA LINKING C9 H15 N2 O9 P U
5MU
Query on 5MU
X RNA LINKING C10 H15 N2 O9 P U

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.5 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-11-14
  • Released Date: 2017-01-11
  • Deposition author(s): Lopez-Alonso, J.P., Fabbretti, A., Kaminishi, T., Iturrioz, I., Brandi, L., Gil Carton, D., Gualerzi, C., Fucini, P., Connell, S.

Revision History

  • Version 1_0: 2017-01-11

    Type: Initial release

  • Version 1_1: 2017-05-03

    Type: Database references

  • Version 1_2: 2017-08-30

    Type: Advisory, Data collection, Derived calculations

  • Version 1_3: 2017-09-13

    Type: Author supporting evidence