9MJ5 | pdb_00009mj5

Catalytic domain of human DNA polymerase alpha in complex with DNA and RPA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history


Literature

The human primosome requires replication protein A when copying DNA with inverted repeats.

Baranovskiy, A.G.Morstadt, L.M.Romero, E.E.Babayeva, N.D.Tahirov, T.H.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf799
  • Primary Citation of Related Structures:  
    9MJ5

  • PubMed Abstract: 

    The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), initiates DNA synthesis on both chromosome strands by generating chimeric RNA-DNA primers for loading DNA polymerases delta and epsilon (Polϵ). Replication protein A (RPA) tightly binds to single-stranded DNA strands, protecting them from nucleolytic digestion and unauthorized transactions. We report here that RPA plays a critical role for the human primosome during DNA synthesis across inverted repeats prone to hairpin formation. On other alternatively structured DNA, forming a G-quadruplex, RPA does not assist primosome. A stimulatory effect of RPA on DNA synthesis across hairpins was also observed for the catalytic domain of Polα but not of Polϵ. The winged helix-turn-helix domain of RPA is essential for an efficient hairpin bypass and increases RPA-Polα cooperativity on the primed DNA template. Cryo-EM studies revealed that this domain is mainly responsible for the interaction between RPA and Polα. The flexible mode of RPA-Polα interaction during DNA synthesis implies the mechanism of template handover between them when the hairpin formation should be avoided. This work provides insight into a cooperative action of RPA and primosome on DNA, which is critical for DNA synthesis across inverted repeats.


  • Organizational Affiliation
    • Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE 68198, United States.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replication protein A 14 kDa subunit121Homo sapiensMutation(s): 0 
Gene Names: RPA3REPA3RPA14
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Find proteins for P35244 (Homo sapiens)
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Go to UniProtKB:  P35244
PHAROS:  P35244
GTEx:  ENSG00000106399 
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UniProt GroupP35244
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Replication protein A 32 kDa subunit236Homo sapiensMutation(s): 0 
Gene Names: RPA2REPA2RPA32RPA34
UniProt & NIH Common Fund Data Resources
Find proteins for P15927 (Homo sapiens)
Explore P15927 
Go to UniProtKB:  P15927
PHAROS:  P15927
GTEx:  ENSG00000117748 
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UniProt GroupP15927
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Replication protein A 70 kDa DNA-binding subunit179Homo sapiensMutation(s): 0 
Gene Names: RPA1REPA1RPA70
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Find proteins for P27694 (Homo sapiens)
Explore P27694 
Go to UniProtKB:  P27694
PHAROS:  P27694
GTEx:  ENSG00000132383 
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UniProt GroupP27694
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunitE [auth S]910Homo sapiensMutation(s): 0 
Gene Names: POLA1POLA
EC: 2.7.7.7
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Find proteins for P09884 (Homo sapiens)
Explore P09884 
Go to UniProtKB:  P09884
PHAROS:  P09884
GTEx:  ENSG00000101868 
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UniProt GroupP09884
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA-DNA primer (11-mer)D [auth P]11Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA template (35-mer)F [auth T]35Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM152032

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 2.0: 2025-03-12
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2025-09-03
    Changes: Data collection, Database references