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 1.2 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: 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 ...

    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.

    Related Citations: 
    • A Conserved Mechanism for Regulating Replisome Disassembly in Eukaryotes.
      Jenkyn-Bedford, M., Jones, M.L., Baris, Y., Labib, K.P.M., Cannone, G., Yeeles, J.T.P., Deegan, T.D.
      (2021) Nature --: --
    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AA [auth B]2,286Homo sapiensMutation(s): 0 
Gene Names: POLE, POLE1
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit 2B [auth A]527Homo sapiensMutation(s): 0 
Gene Names: POLE2, DPE2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]863Homo sapiensMutation(s): 0 
Gene Names: MCM4, CDC21
EC: 3.6.4.12
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6D [auth 6]821Homo sapiensMutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7E [auth 7]719Homo sapiensMutation(s): 0 
Gene Names: MCM7, CDC47, MCM2
EC: 3.6.4.12
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3F [auth 3]808Homo sapiensMutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2G [auth 2]904Homo sapiensMutation(s): 0 
Gene Names: MCM2, BM28, CCNL1, CDCL1, KIAA0030
EC: 3.6.4.12
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5H [auth 5]734Homo sapiensMutation(s): 0 
Gene Names: MCM5, CDC46
EC: 3.6.4.12
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1I [auth D]196Homo sapiensMutation(s): 0 
Gene Names: GINS1, KIAA0186, PSF1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2J [auth E]185Homo sapiensMutation(s): 0 
Gene Names: GINS2, PSF2, CGI-122, DC5, HSPC037
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3K [auth F]216Homo sapiensMutation(s): 0 
Gene Names: GINS3, PSF3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5L [auth G]261Homo sapiensMutation(s): 0 
Gene Names: GINS4, SLD5
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 45 homolog,Cell division control protein 45 homologM [auth C]572Homo sapiensMutation(s): 0 
Gene Names: CDC45, CDC45L, CDC45L2, UNQ374/PRO710
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Protein timeless homologN [auth K]1,208Homo sapiensMutation(s): 0 
Gene Names: TIMELESS, TIM, TIM1, TIMELESS1
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
TIMELESS-interacting proteinO [auth L]338Homo sapiensMutation(s): 0 
Gene Names: TIPIN
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat and HMG-box DNA-binding protein 1Q [auth H],
R [auth I],
S [auth J]		1,160Homo sapiensMutation(s): 0 
Gene Names: WDHD1, AND1
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
ClaspinU [auth Q]1,403Homo sapiensMutation(s): 0 
Gene Names: CLSPN
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Entity ID: 16
MoleculeChainsLengthOrganismImage
Leading strand DNAP [auth M]85Homo sapiens
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Entity ID: 18
MoleculeChainsLengthOrganismImage
Lagging Strand DNAT [auth N]54Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP
Download Ideal Coordinates CCD File 
AA [auth 3],
EA [auth 2],
GA [auth 5]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
SO4 (Subject of Investigation/LOI)
Query on SO4
Download Ideal Coordinates CCD File 
W [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
CA [auth 2],
FA [auth 5],
V [auth B],
X [auth 4],
Y [auth 6],
CA [auth 2],
FA [auth 5],
V [auth B],
X [auth 4],
Y [auth 6],
Z [auth 7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
BA [auth 3],
DA [auth 2],
HA [auth 5]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
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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View more in-depth experimental data
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