3LU0 | pdb_00003lu0

Molecular model of Escherichia coli core RNA polymerase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.

Opalka, N.Brown, J.Lane, W.J.Twist, K.A.Landick, R.Asturias, F.J.Darst, S.A.

(2010) PLoS Biol 8: e1000483

  • DOI: https://doi.org/10.1371/journal.pbio.1000483
  • Primary Citation Related Structures: 
    3LTI, 3LU0

  • PubMed Abstract: 

    The Escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. Nevertheless, a molecular understanding of the details of E. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on E. coli RNA polymerase (RNAP). We use a combination of approaches, including high-resolution X-ray crystallography, ab initio structural prediction, homology modeling, and single-particle cryo-electron microscopy, to generate complete atomic models of E. coli core RNAP and an E. coli RNAP ternary elongation complex. The detailed and comprehensive structural descriptions can be used to help interpret previous biochemical and genetic data in a new light and provide a structural framework for designing experiments to understand the function of the E. coli lineage-specific insertions and their role in the E. coli transcription program.


  • Organizational Affiliation
    • The Rockefeller University, New York, New York, USA.

Macromolecule Content 

  • Total Structure Weight: 389.69 kDa 
  • Atom Count: 25,410 
  • Modeled Residue Count: 3,258 
  • Deposited Residue Count: 3,498 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli K-12Mutation(s): 0 
Gene Names: b3295JW3257pezphsrpoAsez
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Z4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: 
b3987groNJW3950nitBrifronrpoBrpoCstlstv...
b3987groNJW3950nitBrifronrpoBrpoCstlstvtabD

EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Explore P0A8V2 
Go to UniProtKB:  P0A8V2
Entity Groups
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UniProt GroupP0A8V2
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,407Escherichia coli K-12Mutation(s): 0 
Gene Names: b3988JW3951rpoCrpoDtabB
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Explore P0A8T7 
Go to UniProtKB:  P0A8T7
Entity Groups
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UniProt GroupP0A8T7
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega91Escherichia coli K-12Mutation(s): 0 
Gene Names: b3649JW3624rpoZ
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
Entity Groups
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UniProt GroupP0A800
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPARX
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2010-09-29 
  • Deposition Author(s): Darst, S.A.

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-21
    Changes: Database references
  • Version 1.3: 2011-11-23
    Changes: Database references
  • Version 1.4: 2012-02-22
    Changes: Database references
  • Version 1.5: 2018-07-18
    Changes: Data collection
  • Version 1.6: 2024-02-21
    Changes: Data collection, Database references, Derived calculations