5HD9

Crystal Structure of the N-terminal domain of the DNA packaging ATPase from bacteriophage phi29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural and Molecular Basis for Coordination in a Viral DNA Packaging Motor.

Mao, H.Saha, M.Reyes-Aldrete, E.Sherman, M.B.Woodson, M.Atz, R.Grimes, S.Jardine, P.J.Morais, M.C.

(2016) Cell Rep 14: 2017-2029

  • DOI: 10.1016/j.celrep.2016.01.058
  • Primary Citation of Related Structures:  
    5HD9

  • PubMed Abstract: 
  • Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ra ...

    Ring NTPases are a class of ubiquitous molecular motors involved in basic biological partitioning processes. dsDNA viruses encode ring ATPases that translocate their genomes to near-crystalline densities within pre-assembled viral capsids. Here, X-ray crystallography, cryoEM, and biochemical analyses of the dsDNA packaging motor in bacteriophage phi29 show how individual subunits are arranged in a pentameric ATPase ring and suggest how their activities are coordinated to translocate dsDNA. The resulting pseudo-atomic structure of the motor and accompanying functional analyses show how ATP is bound in the ATPase active site; identify two DNA contacts, including a potential DNA translocating loop; demonstrate that a trans-acting arginine finger is involved in coordinating hydrolysis around the ring; and suggest a functional coupling between the arginine finger and the DNA translocating loop. The ability to visualize the motor in action illuminates how the different motor components interact with each other and with their DNA substrate.


    Organizational Affiliation

    Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Encapsidation proteinA194Bacillus virus phi29Mutation(s): 0 
Gene Names: 16gp16
EC: 3.6.4
Find proteins for P11014 (Bacillus phage phi29)
Explore P11014 
Go to UniProtKB:  P11014
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.103α = 90
b = 36.835β = 90
c = 139.017γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
Precognitiondata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM095516
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM059604

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence