3C2P | pdb_00003c2p

X-ray crystal structure of the N4 mini-vRNAP P1 promoter complex

• PDB DOI: https://doi.org/10.2210/pdb3C2P/pdb
• NAKB: 3C2P

• Classification: transferase/DNA
• Organism(s): Enterobacteria phage N4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-01-25 Released: 2008-12-09 
• Deposition Author(s): Gleghorn, M.L., Murakami, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.256 (Depositor) 
• R-Value Work: 
  0.220 (Depositor) 

Literature

Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.

Gleghorn, M.L., Davydova, E.K., Rothman-Denes, L.B., Murakami, K.S.

(2008) Mol Cell 32: 707-717

• PubMed: 19061645 
• DOI: https://doi.org/10.1016/j.molcel.2008.11.010
• Primary Citation Related Structures: 
  3C2P, 3C3L, 3C46


• PubMed Abstract: 
  

  Coliphage N4 virion-encapsidated RNA polymerase (vRNAP) is a member of the phage T7-like single-subunit RNA polymerase (RNAP) family. Its central domain (mini-vRNAP) contains all RNAP functions of the full-length vRNAP, which recognizes a 5 to 7 base pair stem and 3 nucleotide loop hairpin DNA promoter. Here, we report the X-ray crystal structures of mini-vRNAP bound to promoters. Mini-vRNAP uses four structural motifs to recognize DNA sequences at the hairpin loop and stem and to unwind DNA. Despite their low sequence similarity, three out of four motifs are shared with T7 RNAP that recognizes a double-stranded DNA promoter. The binary complex structure and results of engineered disulfide linkage experiments reveal that the plug and motif B loop, which block the access of template DNA to the active site in the apo-form mini-vRNAP, undergo a large-scale conformational change upon promoter binding, explaining the restricted promoter specificity that is critical for N4 phage early transcription.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 266.34 kDa 
• Atom Count: 18,317 
• Modeled Residue Count: 2,225 
• Deposited Residue Count: 2,300 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Virion RNA polymerase	C [auth A], D [auth B]	1,117	N/A	Mutation(s): 0  Gene Names: vRNAP, 50 EC: 2.7.7.6
UniProt
Find proteins for Q859P9 (Enterobacteria phage N4) Explore Q859P9  Go to UniProtKB:  Q859P9

Entity ID: 1
Molecule	Chains	Length	Organism	Image
P1 Promoter DNA	A [auth C], B [auth D]	33	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.256 (Depositor) 
• R-Value Work:  0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.463	α = 90
b = 111.194	β = 90
c = 276.87	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Gleghorn, M.L., Murakami, K.S.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references