3GLG

Crystal Structure of a Mutant (gammaT157A) E. coli Clamp Loader Bound to Primer-Template DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.

Simonetta, K.R.Kazmirski, S.L.Goedken, E.R.Cantor, A.J.Kelch, B.A.McNally, R.Seyedin, S.N.Makino, D.L.O'Donnell, M.Kuriyan, J.

(2009) Cell 137: 659-671

  • DOI: 10.1016/j.cell.2009.03.044
  • Primary Citation of Related Structures:  
    3GLF, 3GLG, 3GLH, 3GLI

  • PubMed Abstract: 
  • Clamp loaders load sliding clamps onto primer-template DNA. The structure of the E. coli clamp loader bound to DNA reveals the formation of an ATP-dependent spiral of ATPase domains that tracks only the template strand, allowing recognition of both RNA and DNA primers ...

    Clamp loaders load sliding clamps onto primer-template DNA. The structure of the E. coli clamp loader bound to DNA reveals the formation of an ATP-dependent spiral of ATPase domains that tracks only the template strand, allowing recognition of both RNA and DNA primers. Unlike hexameric helicases, in which DNA translocation requires distinct conformations of the ATPase domains, the clamp loader spiral is symmetric and is set up to trigger release upon DNA recognition. Specificity for primed DNA arises from blockage of the end of the primer and accommodation of the emerging template along a surface groove. A related structure reveals how the psi protein, essential for coupling the clamp loader to single-stranded DNA-binding protein (SSB), binds to the clamp loader. By stabilizing a conformation of the clamp loader that is consistent with the ATPase spiral observed upon DNA binding, psi binding promotes the clamp-loading activity of the complex.


    Organizational Affiliation

    Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit deltaA, F343Escherichia coli K-12Mutation(s): 0 
Gene Names: holAb0640JW0635
EC: 2.7.7.7
UniProt
Find proteins for P28630 (Escherichia coli (strain K12))
Explore P28630 
Go to UniProtKB:  P28630
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28630
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit tau
B, C, D, G, H, I
B, C, D, G, H, I
395Escherichia coli K-12Mutation(s): 1 
Gene Names: dnaXdnaZdnaZXb0470JW0459
EC: 2.7.7.7
UniProt
Find proteins for P06710 (Escherichia coli (strain K12))
Explore P06710 
Go to UniProtKB:  P06710
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06710
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase III subunit delta'E, J334Escherichia coli K-12Mutation(s): 0 
Gene Names: holBb1099JW1085
EC: 2.7.7.7
UniProt
Find proteins for P28631 (Escherichia coli (strain K12))
Explore P28631 
Go to UniProtKB:  P28631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28631
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*AP*TP*AP*GP*GP*CP*CP*AP*G)-3')K, M 20N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*AP*TP*A)-3')L, N 10N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth G],
FA [auth H],
JA [auth I],
O [auth B],
S [auth C],
BA [auth G],
FA [auth H],
JA [auth I],
O [auth B],
S [auth C],
W [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

Download Ideal Coordinates CCD File 
CA [auth G],
IA [auth I],
KA [auth I],
P [auth B],
T [auth C],
CA [auth G],
IA [auth I],
KA [auth I],
P [auth B],
T [auth C],
X [auth D]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E],
EA [auth G],
HA [auth H],
MA [auth I],
NA [auth J],
AA [auth E],
EA [auth G],
HA [auth H],
MA [auth I],
NA [auth J],
R [auth B],
V [auth C],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth G],
GA [auth H],
LA [auth I],
Q [auth B],
U [auth C],
DA [auth G],
GA [auth H],
LA [auth I],
Q [auth B],
U [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.102α = 90
b = 219.104β = 90
c = 274.664γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-10-10
    Changes: Database references
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations