7PMN

S. cerevisiae replisome-SCF(Dia2) complex bound to double-stranded DNA (conformation II)


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 1.3 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
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]1,009Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1G [auth A]208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF1YDR013WPZA208YD8119.18
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2H [auth B]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF2YJL072CHRF213J1086
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth C]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS5150PACBIOSEQ_LOCUS5239PACBIOSEQ_LOCUS5244PACBIOSEQ_LOCUS5270PACBIOSEQ_LOCUS5331
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth D]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5YDR489W
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 45,Cell division control protein 45K [auth E]657Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha-binding proteinL [auth F],
M [auth G],
N [auth H]
962Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF4CHL15POB1YPR135WP9659.7
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor of kinetochore protein 1Q [auth K]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SKP1CBF3DYDR328CD9798.14
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Protein DIA2R [auth L]735Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DIA2YOR080WYOR29-31
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AS [auth Q]2,222Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BT [auth R]689Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DPB2YPR175WP9705.7
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Topoisomerase 1-associated factor 1U [auth X]1,238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOF1YNL273WN0636
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Chromosome segregation in meiosis protein 3V [auth Y]319Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CSM3YMR048WYM9796.01
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Entity ID: 13
MoleculeChainsLengthOrganismImage
Leading strand template DNAO [auth I]115synthetic construct
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Entity ID: 14
MoleculeChainsLengthOrganismImage
Lagging strand template DNAP [auth J]122Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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: 2021-11-17
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2022-01-05
    Changes: Database references
  • Version 1.3: 2022-01-26
    Changes: Source and taxonomy