6R9B

Cryo-EM structure of bacterial RNAP with a DNA mimic protein Ocr from T7 phage

• PDB DOI: https://doi.org/10.2210/pdb6R9B/pdb
• EM Map EMD-4769: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12, Escherichia phage T7
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-03 Released: 2020-02-26 
• Deposition Author(s): Ye, F.Z., Zhang, X.D.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7

Ye, F.Z., Kotta-Loizou, I., Jovanovic, M., Liu, X.J., Dryden, D.T.F., Buck, M., Zhang, X.D.

(2020) Elife 

• DOI: https://doi.org/10.7554/eLife.52125

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B2C1D1E1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 416.04 kDa 
• Atom Count: 25,880 
• Modelled Residue Count: 3,401 
• Deposited Residue Count: 3,721 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	329	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoA, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A7Z4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,342	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A8V2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,407	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoC, tabB, b3988, JW3951 EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A8T7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	80	Escherichia coli K-12	Mutation(s): 0  Gene Names: rpoZ, SSJG_04328 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A800

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Overcome classical restriction gp0.3	F, G	117	Escherichia phage T7	Mutation(s): 0  Gene Names: 0.3
UniProt
Find proteins for P03775 (Escherichia phage T7) Go to UniProtKB:  P03775

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.10.1
MODEL REFINEMENT	CCP4 package	7

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Ye, F.Z., Zhang, X.D.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/N007816

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release