Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55090.54 
• Atom Count: 3691 
• Residue Count: 328 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2FIO

Phage phi29 transcription regulator p4-DNA complex

• DOI: 10.2210/pdb2FIO/pdb
• NDB: PD0780

• Classification: TRANSCRIPTION/DNA
• Organism(s): Bacillus phage phi29
• Expression System: Escherichia coli


• Deposited: 2005-12-30 Released: 2006-09-26 
• Deposition Author(s): Badia, D., Camacho, A., Perez-Lago, L., Escandon, C., Salas, M., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.279 
• R-Value Work: 0.229 

Literature

The structure of phage phi29 transcription regulator p4-DNA complex reveals an N-hook motif for DNA

Badia, D., Camacho, A., Perez-Lago, L., Escandon, C., Salas, M., Coll, M.

(2006) Mol.Cell 22: 73-81

• PubMed: 16600871 
• DOI: 10.1016/j.molcel.2006.02.019
• Primary Citation of Related Structures:  
  2FIP


• PubMed Abstract: 
  

Protein p4 affects the transcriptional switch that divides bacteriophage phi29 infection in early and late phases. The synthesis of DNA replication proteins and p4 takes place in the early phase, while structural, morphogenesis, and lysis proteins are synthesized in the late phase. Transcriptional switch by p4 is achieved by activating the late promoter A3 and repressing the early promoters A2b and A2c. The crystal structure of p4 alone and in complex with a 41 bp DNA, including the A3 promoter binding site, helps us to understand how the phage cycle is controlled. Protein p4 has a unique alpha/beta fold that includes a DNA recognition motif consisting of two N-terminal beta turn substructures, or N-hooks, located at the tips of an elongated protein homodimer. The two N-hooks enter the major groove of the double helix, establishing base-specific contacts. A high DNA curvature allows p4 N-hooks to reach two major groove areas three helical turns apart, like a bow and its string.

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Organizational Affiliation: 

Institut de Biologia Molecular de Barcelona (CSIC) and Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Late genes activator	A, B	123	Bacillus phage phi29	Mutation(s): 0  Gene Names: 4
Find proteins for P03682 (Bacillus phage phi29) Go to UniProtKB:  P03682

Entity ID: 1
Molecule	Chains	Length	Organism
DNA (41-MER)	C	41	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (41-MER)	D	41	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.279 
• R-Value Work: 0.229 
• Space Group: P 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 52.400	α = 90.00
b = 27.800	β = 97.40
c = 192.800	γ = 90.00

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
XDS	data scaling
CNS	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-30 
• Released Date: 2006-09-26 
• Deposition Author(s): Badia, D., Camacho, A., Perez-Lago, L., Escandon, C., Salas, M., Coll, M.

Revision History 

• Version 1.0: 2006-09-26
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-18
  Type: Advisory, Refinement description