7PFO

Core human replisome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of a human replisome shows the organisation and interactions of a DNA replication machine.

Jones, M.L.Baris, Y.Taylor, M.R.G.Yeeles, J.T.P.

(2021) EMBO J 40: e108819-e108819

  • DOI: https://doi.org/10.15252/embj.2021108819
  • Primary Citation of Related Structures:  
    7PFO

  • PubMed Abstract: 

    The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to unwinding the parental DNA duplex, arranges many proteins including the leading-strand polymerase Pol ε, together with TIMELESS-TIPIN, CLASPIN and AND-1 that have key and varied roles in maintaining smooth replisome progression. How these proteins are coordinated in the human replisome is poorly understood. We have determined a 3.2 Å cryo-EM structure of a human replisome comprising CMG, Pol ε, TIMELESS-TIPIN, CLASPIN and AND-1 bound to replication fork DNA. The structure permits a detailed understanding of how AND-1, TIMELESS-TIPIN and Pol ε engage CMG, reveals how CLASPIN binds to multiple replisome components and identifies the position of the Pol ε catalytic domain. Furthermore, the intricate network of contacts contributed by MCM subunits and TIMELESS-TIPIN with replication fork DNA suggests a mechanism for strand separation.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, 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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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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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 epsilon subunit 2G [auth A]527Homo sapiensMutation(s): 0 
Gene Names: POLE2DPE2
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GTEx:  ENSG00000100479 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AH [auth B]2,286Homo sapiensMutation(s): 0 
Gene Names: POLEPOLE1
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
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GTEx:  ENSG00000177084 
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UniProt GroupQ07864
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45 homologI [auth C]569Homo sapiensMutation(s): 0 
Gene Names: CDC45CDC45LCDC45L2UNQ374/PRO710
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PHAROS:  O75419
GTEx:  ENSG00000093009 
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UniProt GroupO75419
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1J [auth D]196Homo sapiensMutation(s): 0 
Gene Names: GINS1KIAA0186PSF1
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GTEx:  ENSG00000101003 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2K [auth E]185Homo sapiensMutation(s): 0 
Gene Names: GINS2PSF2CGI-122DC5HSPC037
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GTEx:  ENSG00000131153 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3L [auth F]216Homo sapiensMutation(s): 0 
Gene Names: GINS3PSF3
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PHAROS:  Q9BRX5
GTEx:  ENSG00000181938 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5M [auth G]262Homo sapiensMutation(s): 0 
Gene Names: GINS4SLD5
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GTEx:  ENSG00000147536 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat and HMG-box DNA-binding protein 1N [auth H],
O [auth I],
P [auth J]
1,161Homo sapiensMutation(s): 0 
Gene Names: WDHD1AND1
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GTEx:  ENSG00000198554 
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UniProt GroupO75717
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Protein timeless homologQ [auth K]1,209Homo sapiensMutation(s): 0 
Gene Names: TIMELESSTIMTIM1TIMELESS1
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PHAROS:  Q9UNS1
GTEx:  ENSG00000111602 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
TIMELESS-interacting proteinR [auth L]301Homo sapiensMutation(s): 0 
Gene Names: TIPIN
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Find proteins for Q9BVW5 (Homo sapiens)
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PHAROS:  Q9BVW5
GTEx:  ENSG00000075131 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ClaspinU [auth Q]1,371Homo sapiensMutation(s): 0 
Gene Names: CLSPN
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PHAROS:  Q9HAW4
GTEx:  ENSG00000092853 
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Entity ID: 17
MoleculeChains LengthOrganismImage
Leading strand DNAS [auth M]85Homo sapiens
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Entity ID: 18
MoleculeChains LengthOrganismImage
Lagging Strand DNAT [auth N]54Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
CA [auth 5],
X [auth 2],
Y [auth 3]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
GA [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

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AA [auth 4],
BA [auth 5],
EA [auth 6],
FA [auth 7],
V [auth 2]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
DA [auth 5],
W [auth 2],
Z [auth 3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

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: 2021-11-10
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Database references
  • Version 1.2: 2021-12-22
    Changes: Database references
  • Version 2.0: 2023-10-18
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary