7PMK

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


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 2.3 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: PACBIOSEQ_LOCUS187PACBIOSEQ_LOCUS193PACBIOSEQ_LOCUS195PACBIOSEQ_LOCUS196SCNYR20_0007007400SCP684_0007007100MCM2GI527_G0000178
EC: 3.6.4.12
UniProt
Find proteins for A0A6A5Q1S9 (Saccharomyces cerevisiae)
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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
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
DNA helicaseD [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4054PACBIOSEQ_LOCUS4112PACBIOSEQ_LOCUS4129PACBIOSEQ_LOCUS4153PACBIOSEQ_LOCUS4202SCNYR20_0004029000SCP684_0004028600MCM5GI527_G0004088
EC: 3.6.4.12
UniProt
Find proteins for A0A6A5PUY8 (Saccharomyces cerevisiae)
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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: MCM7PACBIOSEQ_LOCUS429
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: PACBIOSEQ_LOCUS944PACBIOSEQ_LOCUS956PACBIOSEQ_LOCUS958SCNYR20_0001022500SCP684_0001022000PSF1GI527_G0000936
UniProt
Find proteins for A0A6A5Q203 (Saccharomyces cerevisiae)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2H [auth B]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3163PACBIOSEQ_LOCUS3191PACBIOSEQ_LOCUS3224PACBIOSEQ_LOCUS3231PACBIOSEQ_LOCUS3255SCNYR20_0009012300SCP684_0009011800PSF2GI527_G0003179
UniProt
Find proteins for A0A6A5PX40 (Saccharomyces cerevisiae)
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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
UniProt
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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: SCNYR20_0005036600
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin ligase complex SCF subunitQ [auth K]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Protein DIA2R [auth L]735Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DIA2YOR080WYOR29-31
UniProt
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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
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BT [auth R]689Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DPB2YPR175WP9705.7
UniProt
Find proteins for P24482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Topoisomerase 1-associated factor 1U [auth X]1,238Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOF1YNL273WN0636
UniProt
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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
UniProt
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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]122synthetic construct
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP (Subject of Investigation/LOI)
Query on ANP

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

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BA [auth 4],
EA [auth 5],
FA [auth 6],
GA [auth 7],
HA [auth Q],
BA [auth 4],
EA [auth 5],
FA [auth 6],
GA [auth 7],
HA [auth Q],
IA [auth Q],
Y [auth 2]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

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AA [auth 3],
DA [auth 5],
X [auth 2]
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 

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 2.0: 2021-11-17
    Changes: Atomic model, Data collection, Derived calculations, Other, Source and taxonomy
  • Version 2.1: 2022-01-05
    Changes: Database references
  • Version 2.2: 2022-01-26
    Changes: Source and taxonomy
  • Version 2.3: 2022-02-02
    Changes: Source and taxonomy