8B9D

Human replisome bound by Pol Alpha


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

How Pol alpha-primase is targeted to replisomes to prime eukaryotic DNA replication.

Jones, M.L.Aria, V.Baris, Y.Yeeles, J.T.P.

(2023) Mol Cell 83: 2911

  • DOI: https://doi.org/10.1016/j.molcel.2023.06.035
  • Primary Citation of Related Structures:  
    8B9A, 8B9B, 8B9C, 8B9D

  • PubMed Abstract: 

    During eukaryotic DNA replication, Pol α-primase generates primers at replication origins to start leading-strand synthesis and every few hundred nucleotides during discontinuous lagging-strand replication. How Pol α-primase is targeted to replication forks to prime DNA synthesis is not fully understood. Here, by determining cryoelectron microscopy (cryo-EM) structures of budding yeast and human replisomes containing Pol α-primase, we reveal a conserved mechanism for the coordination of priming by the replisome. Pol α-primase binds directly to the leading edge of the CMG (CDC45-MCM-GINS) replicative helicase via a complex interaction network. The non-catalytic PRIM2/Pri2 subunit forms two interfaces with CMG that are critical for in vitro DNA replication and yeast cell growth. These interactions position the primase catalytic subunit PRIM1/Pri1 directly above the exit channel for lagging-strand template single-stranded DNA (ssDNA), revealing why priming occurs efficiently only on the lagging-strand template and elucidating a mechanism for Pol α-primase to overcome competition from RPA to initiate primer synthesis.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]904Homo sapiensMutation(s): 0 
Gene Names: MCM2BM28CCNL1CDCL1KIAA0030
EC: 3.6.4.12
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Find proteins for P49736 (Homo sapiens)
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PHAROS:  P49736
GTEx:  ENSG00000073111 
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UniProt GroupP49736
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]808Homo sapiensMutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
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PHAROS:  P25205
GTEx:  ENSG00000112118 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]863Homo sapiensMutation(s): 0 
Gene Names: MCM4CDC21
EC: 3.6.4.12
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GTEx:  ENSG00000104738 
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UniProt GroupP33991
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5D [auth 5]734Homo sapiensMutation(s): 0 
Gene Names: MCM5CDC46
EC: 3.6.4.12
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GTEx:  ENSG00000100297 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]821Homo sapiensMutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
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GTEx:  ENSG00000076003 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]719Homo sapiensMutation(s): 0 
Gene Names: MCM7CDC47MCM2
EC: 3.6.4.12
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GTEx:  ENSG00000166508 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha subunit BG [auth A]598Homo sapiensMutation(s): 0 
Gene Names: POLA2
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GTEx:  ENSG00000014138 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45 homologH [auth C]569Homo sapiensMutation(s): 0 
Gene Names: CDC45CDC45LCDC45L2UNQ374/PRO710
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GTEx:  ENSG00000093009 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1I [auth D]196Homo sapiensMutation(s): 0 
Gene Names: GINS1KIAA0186PSF1
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GTEx:  ENSG00000101003 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2J [auth E]185Homo sapiensMutation(s): 0 
Gene Names: GINS2PSF2CGI-122DC5HSPC037
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GTEx:  ENSG00000131153 
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UniProt GroupQ9Y248
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3K [auth F]216Homo sapiensMutation(s): 0 
Gene Names: GINS3PSF3
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PHAROS:  Q9BRX5
GTEx:  ENSG00000181938 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5L [auth G]261Homo sapiensMutation(s): 0 
Gene Names: GINS4SLD5
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PHAROS:  Q9BRT9
GTEx:  ENSG00000147536 
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UniProt GroupQ9BRT9
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Protein timeless homologM [auth K]1,209Homo sapiensMutation(s): 0 
Gene Names: TIMELESSTIMTIM1TIMELESS1
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PHAROS:  Q9UNS1
GTEx:  ENSG00000111602 
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UniProt GroupQ9UNS1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
TIMELESS-interacting proteinN [auth L]301Homo sapiensMutation(s): 0 
Gene Names: TIPIN
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GTEx:  ENSG00000075131 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase large subunitQ [auth P]509Homo sapiensMutation(s): 0 
Gene Names: PRIM2PRIM2A
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GTEx:  ENSG00000146143 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ClaspinR [auth Q]1,371Homo sapiensMutation(s): 0 
Gene Names: CLSPN
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Find proteins for Q9HAW4 (Homo sapiens)
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PHAROS:  Q9HAW4
GTEx:  ENSG00000092853 
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UniProt GroupQ9HAW4
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
DNA primase small subunitS [auth O]462Homo sapiensMutation(s): 0 
Gene Names: PRIM1
EC: 2.7.7.102
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GTEx:  ENSG00000198056 
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UniProt GroupP49642
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat and HMG-box DNA-binding protein 1T [auth H],
V [auth J],
W [auth I]
1,160Homo sapiensMutation(s): 0 
Gene Names: WDHD1AND1
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GTEx:  ENSG00000198554 
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UniProt GroupO75717
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha catalytic subunitU [auth B]1,504Homo sapiensMutation(s): 0 
Gene Names: POLA1POLA
EC: 2.7.7.7
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Find proteins for P09884 (Homo sapiens)
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PHAROS:  P09884
GTEx:  ENSG00000101868 
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UniProt GroupP09884
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Entity ID: 15
MoleculeChains LengthOrganismImage
Leading strand DNAO [auth M]84Homo sapiens
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA MoleculeP [auth N]86Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

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DA [auth 5],
X [auth 2],
Z [auth 3]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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BA [auth 4],
CA [auth 5],
FA [auth 6],
GA [auth 7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth 3],
EA [auth 5],
Y [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20_4459:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/12

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references