3FLO

Crystal structure of the carboxyl-terminal domain of yeast DNA polymerase alpha in complex with its B subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

3D architecture of DNA Pol alpha reveals the functional core of multi-subunit replicative polymerases

Klinge, S.Nunez-Ramirez, R.Llorca, O.Pellegrini, L.

(2009) EMBO J 28: 1978-1987

  • DOI: 10.1038/emboj.2009.150
  • Primary Citation of Related Structures:  
    3FLO

  • PubMed Abstract: 
  • Eukaryotic DNA replication requires the coordinated activity of the multi-subunit DNA polymerases: Pol alpha, Pol delta and Pol epsilon. The conserved catalytic and regulatory B subunits associate in a constitutive heterodimer that represents the functional core of all three replicative polymerases ...

    Eukaryotic DNA replication requires the coordinated activity of the multi-subunit DNA polymerases: Pol alpha, Pol delta and Pol epsilon. The conserved catalytic and regulatory B subunits associate in a constitutive heterodimer that represents the functional core of all three replicative polymerases. Here, we combine X-ray crystallography and electron microscopy (EM) to describe subunit interaction and 3D architecture of heterodimeric yeast Pol alpha. The crystal structure of the C-terminal domain (CTD) of the catalytic subunit bound to the B subunit illustrates a conserved mechanism of accessory factor recruitment by replicative polymerases. The EM reconstructions of Pol alpha reveal a bilobal shape with separate catalytic and regulatory modules. Docking of the B-CTD complex in the EM reconstruction shows that the B subunit is tethered to the polymerase domain through a structured but flexible linker. Our combined findings provide a structural template for the common functional architecture of the three major replicative DNA polymerases.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, Cambridge, UK.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha subunit BA,
D [auth C],
G [auth E],
J [auth G]
460Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL12
UniProt
Find proteins for P38121 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P38121
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38121
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit AB [auth I],
E [auth J],
H [auth K],
K [auth L]
3Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL1CDC17
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunit AC [auth B],
F [auth D],
I [auth F],
L [auth H]
206Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL1CDC17
EC: 2.7.7.7
UniProt
Find proteins for P13382 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13382 
Go to UniProtKB:  P13382
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13382
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth E],
AC [auth G],
BA [auth B],
BB [auth E],
CA [auth B],
AB [auth E],
AC [auth G],
BA [auth B],
BB [auth E],
CA [auth B],
CB [auth E],
DA [auth B],
DB [auth E],
DC [auth H],
EA [auth B],
EB [auth E],
EC [auth H],
FA [auth B],
FB [auth E],
FC [auth H],
GA [auth B],
GB [auth E],
GC [auth H],
HA [auth C],
HB [auth E],
IA [auth C],
IB [auth E],
JA [auth C],
JB [auth E],
KA [auth C],
LA [auth C],
M [auth A],
MA [auth C],
MB [auth F],
N [auth A],
NA [auth C],
NB [auth F],
O [auth A],
OA [auth C],
OB [auth F],
P [auth A],
PA [auth C],
PB [auth F],
Q [auth A],
QA [auth C],
QB [auth G],
R [auth A],
RA [auth C],
RB [auth G],
S [auth A],
SB [auth G],
T [auth A],
TB [auth G],
U [auth A],
UA [auth D],
UB [auth G],
V [auth A],
VA [auth D],
VB [auth G],
W [auth A],
WA [auth D],
WB [auth G],
X [auth A],
XA [auth D],
XB [auth G],
Y [auth A],
YA [auth E],
YB [auth G],
ZA [auth E],
ZB [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B],
BC [auth H],
CC [auth H],
KB [auth F],
LB [auth F],
AA [auth B],
BC [auth H],
CC [auth H],
KB [auth F],
LB [auth F],
SA [auth D],
TA [auth D],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.411α = 90
b = 142.633β = 102.33
c = 175.255γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-09-05
    Changes: Derived calculations