7PLO

H. sapiens replisome-CUL2/LRR1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


Literature

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 600: 743-747

  • DOI: https://doi.org/10.1038/s41586-021-04145-3
  • Primary Citation of Related Structures:  
    7PLO, 7PMK, 7PMN

  • PubMed Abstract: 

    Replisome disassembly is the final step of eukaryotic DNA replication and is triggered by ubiquitylation of the CDC45-MCM-GINS (CMG) replicative helicase 1-3 . Despite being driven by evolutionarily diverse E3 ubiquitin ligases in different eukaryotes (SCF Dia2 in budding yeast 1 , CUL2 LRR1 in metazoa 4-7 ), replisome disassembly is governed by a common regulatory principle, in which ubiquitylation of CMG is suppressed before replication termination, to prevent replication fork collapse. Recent evidence suggests that this suppression is mediated by replication fork DNA 8-10 . However, it is unknown how SCF Dia2 and CUL2 LRR1 discriminate terminated from elongating replisomes, to selectively ubiquitylate CMG only after termination. Here we used cryo-electron microscopy to solve high-resolution structures of budding yeast and human replisome-E3 ligase assemblies. Our structures show that the leucine-rich repeat domains of Dia2 and LRR1 are structurally distinct, but bind to a common site on CMG, including the MCM3 and MCM5 zinc-finger domains. The LRR-MCM interaction is essential for replisome disassembly and, crucially, is occluded by the excluded DNA strand at replication forks, establishing the structural basis for the suppression of CMG ubiquitylation before termination. Our results elucidate a conserved mechanism for the regulation of replisome disassembly in eukaryotes, and reveal a previously unanticipated role for DNA in preserving replisome integrity.


  • 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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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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Find proteins for P25205 (Homo sapiens)
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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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Find proteins for P33991 (Homo sapiens)
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PHAROS:  P33991
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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UniProt GroupP33992
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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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UniProt GroupQ14566
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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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Find proteins for P56282 (Homo sapiens)
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PHAROS:  P56282
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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Find proteins for Q07864 (Homo sapiens)
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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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Find proteins for O75419 (Homo sapiens)
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PHAROS:  O75419
GTEx:  ENSG00000093009 
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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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Find proteins for Q14691 (Homo sapiens)
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PHAROS:  Q14691
GTEx:  ENSG00000101003 
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UniProt GroupQ14691
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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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Find proteins for Q9Y248 (Homo sapiens)
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GTEx:  ENSG00000131153 
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UniProt GroupQ9Y248
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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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Find proteins for Q9BRX5 (Homo sapiens)
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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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Find proteins for Q9BRT9 (Homo sapiens)
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PHAROS:  Q9BRT9
GTEx:  ENSG00000147536 
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UniProt GroupQ9BRT9
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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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Find proteins for O75717 (Homo sapiens)
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PHAROS:  O75717
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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Find proteins for Q9UNS1 (Homo sapiens)
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PHAROS:  Q9UNS1
GTEx:  ENSG00000111602 
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UniProt GroupQ9UNS1
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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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UniProt GroupQ9BVW5
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat protein 1U [auth O]414Homo sapiensMutation(s): 0 
Gene Names: LRR1PPIL5
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Find proteins for Q96L50 (Homo sapiens)
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PHAROS:  Q96L50
GTEx:  ENSG00000165501 
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UniProt GroupQ96L50
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BV [auth P]118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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Find proteins for Q15370 (Homo sapiens)
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PHAROS:  Q15370
GTEx:  ENSG00000103363 
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UniProt GroupQ15370
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ClaspinW [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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CX [auth R]112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Find proteins for Q15369 (Homo sapiens)
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PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-2Y [auth S]745Homo sapiensMutation(s): 0 
Gene Names: CUL2
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Find proteins for Q13617 (Homo sapiens)
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PHAROS:  Q13617
GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1Z [auth T]108Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
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GTEx:  ENSG00000100387 
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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]41Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

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CA [auth 2],
DA [auth 3],
GA [auth 5]
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 
LA [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)
Query on ZN

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AA [auth 2]
FA [auth 4]
HA [auth 5]
JA [auth 6]
KA [auth 7]
AA [auth 2],
FA [auth 4],
HA [auth 5],
JA [auth 6],
KA [auth 7],
MA [auth T],
NA [auth T],
OA [auth T]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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BA [auth 2],
EA [auth 3],
IA [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2

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
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_12016/13
Wellcome TrustUnited Kingdom204678/Z/16/Z

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-10
    Type: Initial release
  • Version 1.1: 2022-01-05
    Changes: Database references
  • Version 2.0: 2022-07-06
    Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 3.0: 2023-10-18
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary