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 2.0 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: 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 ...

    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 Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK. tdeegan@ed.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ClaspinA [auth Q]1,371Homo sapiensMutation(s): 0 
Gene Names: CLSPN
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2B [auth 2]904Homo sapiensMutation(s): 0 
Gene Names: MCM2, BM28, CCNL1, CDCL1, KIAA0030
EC: 3.6.4.12
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3C [auth 3]808Homo sapiensMutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4D [auth 4]863Homo sapiensMutation(s): 0 
Gene Names: MCM4, CDC21
EC: 3.6.4.12
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5E [auth 5]734Homo sapiensMutation(s): 0 
Gene Names: MCM5, CDC46
EC: 3.6.4.12
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6F [auth 6]821Homo sapiensMutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7G [auth 7]719Homo sapiensMutation(s): 0 
Gene Names: MCM7, CDC47, MCM2
EC: 3.6.4.12
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit 2H [auth A]527Homo sapiensMutation(s): 0 
Gene Names: POLE2, DPE2
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AI [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: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 45 homologJ [auth C]569Homo sapiensMutation(s): 0 
Gene Names: CDC45, CDC45L, CDC45L2, UNQ374/PRO710
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1K [auth D]196Homo sapiensMutation(s): 0 
Gene Names: GINS1, KIAA0186, PSF1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2L [auth E]185Homo sapiensMutation(s): 0 
Gene Names: GINS2, PSF2, CGI-122, DC5, HSPC037
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3M [auth F]216Homo sapiensMutation(s): 0 
Gene Names: GINS3, PSF3
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5N [auth G]262Homo sapiensMutation(s): 0 
Gene Names: GINS4, SLD5
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat and HMG-box DNA-binding protein 1O [auth H],
P [auth I],
Q [auth J]		1,161Homo sapiensMutation(s): 0 
Gene Names: WDHD1, AND1
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UniProt GroupO75717
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Protein timeless homologR [auth K]1,209Homo sapiensMutation(s): 0 
Gene Names: TIMELESS, TIM, TIM1, TIMELESS1
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
TIMELESS-interacting proteinS [auth L]301Homo sapiensMutation(s): 0 
Gene Names: TIPIN
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Leucine-rich repeat protein 1V [auth O]414Homo sapiensMutation(s): 0 
Gene Names: LRR1, PPIL5
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-BW [auth P]118Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-CX [auth R]112Homo sapiensMutation(s): 0 
Gene Names: ELOC, TCEB1
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-2Y [auth S]759Homo sapiensMutation(s): 0 
Gene Names: CUL2
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1Z [auth T]108Homo sapiensMutation(s): 0 
Gene Names: RBX1, RNF75, ROC1
EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
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Entity ID: 18
MoleculeChainsLengthOrganismImage
Leading strand DNAT [auth M]85Homo sapiens
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Entity ID: 19
MoleculeChainsLengthOrganismImage
Lagging strand DNAU [auth N]41Homo sapiens
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
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		 Ligand Interaction
SO4 (Subject of Investigation/LOI)
Query on SO4
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LA [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
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 B],
NA [auth T],
OA [auth T],
PA [auth T]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
BA [auth 2],
EA [auth 3],
IA [auth 5]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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