3U5Z

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

How a DNA polymerase clamp loader opens a sliding clamp.

Kelch, B.A.Makino, D.L.O'Donnell, M.Kuriyan, J.

(2011) Science 334: 1675-1680

  • DOI: 10.1126/science.1211884
  • Primary Citation of Related Structures:  3U60, 3U61

  • PubMed Abstract: 
  • Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the ...

    Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.


    Organizational Affiliation

    Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase accessory protein 44
B, C, D, E, L, M, N, O
324Enterobacteria phage T4Gene Names: 44
Find proteins for P04526 (Enterobacteria phage T4)
Go to UniProtKB:  P04526
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase accessory protein 62
A, K
199Enterobacteria phage T4Gene Names: 62
Find proteins for P04527 (Enterobacteria phage T4)
Go to UniProtKB:  P04527
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase processivity component
G, H, F, Q, R, P
228Enterobacteria phage T4Gene Names: 45
Find proteins for P04525 (Enterobacteria phage T4)
Go to UniProtKB:  P04525
Entity ID: 4
MoleculeChainsLengthOrganism
Template DNA strandI,S30N/A
Entity ID: 5
MoleculeChainsLengthOrganism
Primer DNA strandJ,T20N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
E, O
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B, C, D, E, L, M, N, O
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
08T
Query on 08T

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Download CCD File 
B, C, D, L, M, N
[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
C10 H14 Be F3 N5 O10 P2
WOGYHYSOODLXII-KWIZKVQNSA-J
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
F, G, H, P, Q, R
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 95.702α = 90.00
b = 239.177β = 90.00
c = 247.672γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
AutoSolphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release