3IYD

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Structural Biology Knowledgebase: 3IYD SBKB.org


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.8 Å
  • Aggregation State: Particle
  • Specimen Type: Negative Staining
  • Reconstruction Method: Single Particle

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IYD

Classification: TRANSCRIPTION / DNA

Total Structure Weight: 568641.71


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-directed RNA polymerase subunit alpha A, B 329 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoA pez phs sez b3295 JW3257
DNA-directed RNA polymerase subunit beta C 1342 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoB groN nitB rif ron stl stv tabD b3987 JW3950
DNA-directed RNA polymerase subunit beta D 1413 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoC tabB b3988 JW3951
DNA-directed RNA polymerase subunit omega E 90 Escherichia coli EC#: 2.7.7.6 IUBMB
Gene Name(s): rpoZ b3649 JW3624
RNA polymerase sigma factor rpoD F 613 Escherichia coli Mutation: D149N, Y571H
Gene Name(s): rpoD alt b3067 JW3039
Catabolite gene activator G, H 209 Escherichia coli Gene Name(s): crp cap csm b3357 JW5702
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (98-MER) I 98 synthetic
DNA (98-MER) J 98 synthetic

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

G, H ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
CYCLIC AMP; CAMP (Synonym)
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CMP IC50: 129690 nM (95) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.8 Å
  • Aggregation State: Particle
  • Specimen Type: Negative Staining
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-08-01
  • Released Date: 2009-11-10
  • Deposition author(s): Hudson, B.P., Quispe, J., Lara, S., Kim, Y., Berman, H., Arnold, E., Ebright, R.H., Lawson, C.L.

Revision History

  • 2016-02-10
    Type: Polymer description | Details: Corrected polymer information
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name