Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 114.03 kDa 
• Atom Count: 7540 
• Modelled Residue Count: 876 
• Deposited Residue Count: 931 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

1S77

T7 RNAP product pyrophosphate elongation complex

• PDB DOI: 10.2210/pdb1S77/pdb
• NDB: PH0010

• Classification: TRANSFERASE
• Organism(s): Escherichia phage T7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-29 Released: 2004-03-23 
• Deposition Author(s): Yin, Y.W., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.285 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 

Literature

The structural mechanism of translocation and helicase activity in T7 RNA polymerase.

Yin, Y.W., Steitz, T.A.

(2004) Cell 116: 393-404

• PubMed: 15016374 
• DOI: 10.1016/s0092-8674(04)00120-5
• Primary Citation of Related Structures:  
  1S76, 1S77


• PubMed Abstract: 
  

RNA polymerase functions like a molecular motor that can convert chemical energy into the work of strand separation and translocation along the DNA during transcription. The structures of phage T7 RNA polymerase in an elongation phase substrate complex that includes the incoming nucleoside triphosphate and a pretranslocation product complex that includes the product pyrophosphate (PPi) are described here. These structures and the previously determined posttranslocation elongation complex demonstrate that two enzyme conformations exist during a cycle of single nucleotide addition. One orientation of a five-helix subdomain is stabilized by the phosphates of either the incoming NTP or by the product PPi. A second orientation of this subdomain is stable in their absence and is associated with translocation of the heteroduplex product as well as strand separation of the downstream DNA. We propose that the dissociation of the product PPi after nucleotide addition produces the protein conformational change resulting in translocation and strand separation.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Macromolecules

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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*GP*TP*GP*TP*T)-3')	A [auth T]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*AP*CP*GP*TP*TP*GP*CP*GP*CP*AP*CP*GP*GP*C)-3')	B [auth N]	17	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*CP*AP*CP*GP*GP*CP*GP*AP*(3DA))-3')	C [auth R]	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	G [auth D]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG	E [auth R], F [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.285 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.738	α = 90
b = 141.843	β = 90
c = 142.856	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-29 
• Released Date: 2004-03-23 
Deposition Author(s): Yin, Y.W., Steitz, T.A.

Revision History  

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance