6PB4

The E. coli class-II CAP-dependent transcription activation complex with de novo RNA transcript at the state 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Visualization of two architectures in class-II CAP-dependent transcription activation

Shi, W.Jiang, Y.Deng, Y.Dong, Z.Liu, B.

(2020) PLoS Biol 18: e3000706


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B329Escherichia coliMutation(s): 0 
Gene Names: rpoAZ4665ECs4160
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1342Escherichia coliMutation(s): 0 
Gene Names: rpoBECS88_4448
EC: 2.7.7.6
UniProt
Find proteins for B7MIX3 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Explore B7MIX3 
Go to UniProtKB:  B7MIX3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1407Escherichia coliMutation(s): 0 
Gene Names: rpoCZ5561ECs4911
EC: 2.7.7.6
UniProt
Find proteins for P0A8T8 (Escherichia coli O157:H7)
Explore P0A8T8 
Go to UniProtKB:  P0A8T8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE91Escherichia coliMutation(s): 0 
Gene Names: rpoZECS88_4064
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor RpoDF628Escherichia coliMutation(s): 0 
Gene Names: rpoDaltb3067JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
Explore P00579 
Go to UniProtKB:  P00579
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-activated global transcriptional regulator CRPG, H210Escherichia coliMutation(s): 0 
Gene Names: crpZ4718ECs4208
UniProt
Find proteins for P0ACK0 (Escherichia coli O157:H7)
Explore P0ACK0 
Go to UniProtKB:  P0ACK0
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
SYNTHETIC NONTEMPLATE STRAND DNA (78-MER)I [auth 1]78Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsLengthOrganismImage
SYNTHETIC TEMPLATE STRAND DNA (78-MER)J [auth 2]78Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 9
    MoleculeChainsLengthOrganismImage
    Nascent RNAK [auth 3]3Escherichia coli
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CMP
    Query on CMP

    Download Ideal Coordinates CCD File 
    O [auth G], P [auth H]ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
    C10 H12 N5 O6 P
    IVOMOUWHDPKRLL-KQYNXXCUSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    L [auth D], M [auth D]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    N [auth D]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 4.35 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2019-06-13 
    • Released Date: 2020-03-18 
    • Deposition Author(s): Liu, B., Shi, W.

    Revision History  (Full details and data files)

    • Version 1.0: 2020-03-18
      Type: Initial release
    • Version 1.1: 2020-04-29
      Changes: Database references
    • Version 1.2: 2021-02-10
      Changes: Derived calculations, Source and taxonomy