Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 113.54 kDa 
• Atom Count: 7956 
• Residue Count: 910 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

1MSW

Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase

• DOI: 10.2210/pdb1MSW/pdb
• NDB: PD0345

• Classification: TRANSCRIPTION/DNA/RNA
• Organism(s): Escherichia phage T7
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-09-19 Released: 2002-11-15 
• Deposition Author(s): Yin, Y.W., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.275 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Literature

Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase

Yin, Y.W., Steitz, T.A.

(2002) Science 298: 1387-1395

• PubMed: 12242451 
• DOI: 10.1126/science.1077464
• Structures With Same Primary Citation


• PubMed Abstract: 
  

To make messenger RNA transcripts, bacteriophage T7 RNA polymerase (T7 RNAP) undergoes a transition from an initiation phase, which only makes short RNA fragments, to a stable elongation phase. We have determined at 2.1 angstrom resolution the crystal structure of a T7 RNAP elongation complex with 30 base pairs of duplex DNA containing a "transcription bubble" interacting with a 17-nucleotide RNA transcript. The transition from an initiation to an elongation complex is accompanied by a major refolding of the amino-terminal 300 residues. This results in loss of the promoter binding site, facilitating promoter clearance, and creates a tunnel that surrounds the RNA transcript after it peels off a seven-base pair heteroduplex. Formation of the exit tunnel explains the enhanced processivity of the elongation complex. Downstream duplex DNA binds to the fingers domain, and its orientation relative to upstream DNA in the initiation complex implies an unwinding that could facilitate formation of the open promoter complex.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase	D	883	Escherichia phage T7	Mutation(s): 0  Gene Names: 1 EC: 2.7.7.6
Find proteins for P00573 (Escherichia phage T7) Go to UniProtKB:  P00573

Entity ID: 1
Molecule	Chains	Length	Organism
Template DNA	T	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
Non-Template DNA	N	17	N/A

Entity ID: 3
Molecule	Chains	Length	Organism
RNA message	R	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.275 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.91	α = 90
b = 145.46	β = 90
c = 145.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-09-19 
• Released Date: 2002-11-15 
Deposition Author(s): Yin, Y.W., Steitz, T.A.

Revision History 

• Version 1.0: 2002-11-15
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance