8QJ7

Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

CryoEM insights into RNA primer synthesis by the human primosome.

Yin, Z.Kilkenny, M.L.Ker, D.S.Pellegrini, L.

(2024) FEBS J 

  • DOI: https://doi.org/10.1111/febs.17082
  • Primary Citation of Related Structures:  
    8QJ7

  • PubMed Abstract: 

    Eukaryotic DNA replication depends on the primosome - a complex of DNA polymerase alpha (Pol α) and primase - to initiate DNA synthesis by polymerisation of an RNA-DNA primer. Primer synthesis requires the tight coordination of primase and polymerase activities. Recent cryo-electron microscopy (cryoEM) analyses have elucidated the extensive conformational transitions required for RNA primer handover between primase and Pol α and primer elongation by Pol α. Because of the intrinsic flexibility of the primosome, however, structural information about the initiation of RNA primer synthesis is still lacking. Here, we capture cryoEM snapshots of the priming reaction to reveal the conformational trajectory of the human primosome that brings DNA primase subunits 1 and 2 (PRIM1 and PRIM2, respectively) together, poised for RNA synthesis. Furthermore, we provide experimental evidence for the continuous association of primase subunit PRIM2 with the RNA primer during primer synthesis, and for how both initiation and termination of RNA primer polymerisation are licenced by specific rearrangements of DNA polymerase alpha catalytic subunit (POLA1), the polymerase subunit of Pol α. Our findings fill a critical gap in our understanding of the conformational changes that underpin the synthesis of the RNA primer by the primosome. Together with existing evidence, they provide a complete description of the structural dynamics of the human primosome during DNA replication initiation.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunitA [auth C]420Homo sapiensMutation(s): 0 
Gene Names: PRIM1
UniProt & NIH Common Fund Data Resources
Find proteins for P49642 (Homo sapiens)
Explore P49642 
Go to UniProtKB:  P49642
PHAROS:  P49642
GTEx:  ENSG00000198056 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49642
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunitB [auth A]1,462Homo sapiensMutation(s): 0 
Gene Names: POLA1
UniProt & NIH Common Fund Data Resources
Find proteins for P09884 (Homo sapiens)
Explore P09884 
Go to UniProtKB:  P09884
PHAROS:  P09884
GTEx:  ENSG00000101868 
Entity Groups  
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UniProt GroupP09884
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha subunit BC [auth B]598Homo sapiensMutation(s): 0 
Gene Names: POLA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14181 (Homo sapiens)
Explore Q14181 
Go to UniProtKB:  Q14181
PHAROS:  Q14181
GTEx:  ENSG00000014138 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14181
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunit509Homo sapiensMutation(s): 0 
Gene Names: PRIM2PRIM2A
UniProt & NIH Common Fund Data Resources
Find proteins for P49643 (Homo sapiens)
Explore P49643 
Go to UniProtKB:  P49643
PHAROS:  P49643
GTEx:  ENSG00000146143 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49643
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
H [auth C]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
K [auth D]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
E [auth C],
I [auth A],
J [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
F [auth C],
G [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom221892/Z/20/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release