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- PDB-5xf8: Cryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state -

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Basic information

Entry
Database: PDB / ID: 5xf8
TitleCryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state
DescriptorMinichromosome maintenance protein 5
Cell division cycle protein CDT1
(DNA replication licensing factor ...) x 5
KeywordsHYDROLASE / helicase / DNA replication
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (7.1 Å resolution / Particle / Single particle)
AuthorsZhai, Y. / Cheng, E. / Wu, H. / Li, N. / Yung, P.Y. / Gao, N. / Tye, B.K.
CitationNat. Struct. Mol. Biol., 2017, 24, 300-308

Nat. Struct. Mol. Biol., 2017, 24, 300-308 Yorodumi Papers
Open-ringed structure of the Cdt1-Mcm2-7 complex as a precursor of the MCM double hexamer.
Yuanliang Zhai / Erchao Cheng / Hao Wu / Ningning Li / Philip Yuk Kwong Yung / Ning Gao / Bik-Kwoon Tye

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 9, 2017 / Release: May 3, 2017

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Assembly

Deposited unit
2: DNA replication licensing factor MCM2
3: DNA replication licensing factor MCM3
4: DNA replication licensing factor MCM4
5: Minichromosome maintenance protein 5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
C: Cell division cycle protein CDT1


Theoretical massNumber of molelcules
Total (without water)677,9767
Polyers677,9767
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA replication licensing factor ... , 5 types, 5 molecules 23467

#1: Polypeptide(L)DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2


Mass: 98911.539 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P29469, EC: 3.6.4.12

Cellular component

Molecular function

Biological process

  • cellular response to DNA damage stimulus (GO: 0006974)
  • DNA strand elongation involved in DNA replication (GO: 0006271)
  • DNA unwinding involved in DNA replication (GO: 0006268)
  • double-strand break repair via break-induced replication (GO: 0000727)
  • mitotic DNA replication initiation (GO: 1902975)
  • negative regulation of ATP-dependent DNA helicase activity (GO: 1902450)
  • pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO: 0006267)
  • regulation of cell proliferation (GO: 0042127)
#2: Polypeptide(L)DNA replication licensing factor MCM3 / Minichromosome maintenance protein 3


Mass: 110774.703 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P24279, EC: 3.6.4.12

Cellular component

Molecular function

Biological process

  • chromatin silencing at silent mating-type cassette (GO: 0030466)
  • chromatin silencing at telomere (GO: 0006348)
  • DNA duplex unwinding (GO: 0032508)
  • DNA replication initiation (GO: 0006270)
  • DNA strand elongation involved in DNA replication (GO: 0006271)
  • double-strand break repair via break-induced replication (GO: 0000727)
  • mitotic DNA replication initiation (GO: 1902975)
  • pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO: 0006267)
#3: Polypeptide(L)DNA replication licensing factor MCM4 / Cell division control protein 54


Mass: 105138.375 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P30665, EC: 3.6.4.12

Cellular component

Molecular function

Biological process

  • DNA replication initiation (GO: 0006270)
  • DNA strand elongation involved in DNA replication (GO: 0006271)
  • DNA unwinding involved in DNA replication (GO: 0006268)
  • double-strand break repair via break-induced replication (GO: 0000727)
  • nuclear DNA replication (GO: 0033260)
  • pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO: 0006267)
#5: Polypeptide(L)DNA replication licensing factor MCM6 / Minichromosome maintenance protein 6


Mass: 113110.211 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P53091, EC: 3.6.4.12

Cellular component

Molecular function

Biological process

  • DNA replication initiation (GO: 0006270)
  • DNA strand elongation involved in DNA replication (GO: 0006271)
  • DNA unwinding involved in DNA replication (GO: 0006268)
  • double-strand break repair via break-induced replication (GO: 0000727)
  • pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO: 0006267)
#6: Polypeptide(L)DNA replication licensing factor MCM7 / Cell division control protein 47 / Minichromosome maintenance protein 7


Mass: 95049.875 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38132, EC: 3.6.4.12

Cellular component

Molecular function

Biological process

  • chromatin silencing at silent mating-type cassette (GO: 0030466)
  • chromatin silencing at telomere (GO: 0006348)
  • DNA replication initiation (GO: 0006270)
  • DNA strand elongation involved in DNA replication (GO: 0006271)
  • DNA unwinding involved in DNA replication (GO: 0006268)
  • double-strand break repair via break-induced replication (GO: 0000727)
  • nuclear DNA replication (GO: 0033260)
  • pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO: 0006267)

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Polypeptide(L) , 2 types, 2 molecules 5C

#4: Polypeptide(L)Minichromosome maintenance protein 5 / Cell division control protein 46


Mass: 86505.734 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P29496, EC: 3.6.4.12

Cellular component

Molecular function

Biological process

  • chromatin silencing at telomere (GO: 0006348)
  • DNA replication initiation (GO: 0006270)
  • DNA strand elongation involved in DNA replication (GO: 0006271)
  • double-strand break repair via break-induced replication (GO: 0000727)
  • establishment of chromatin silencing (GO: 0006343)
  • negative regulation of chromatin silencing at telomere (GO: 0031939)
  • nuclear DNA replication (GO: 0033260)
  • pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO: 0006267)
  • regulation of DNA-dependent DNA replication initiation (GO: 0030174)
#7: Polypeptide(L)Cell division cycle protein CDT1 / SIC1 indispensable protein 2 / Topoisomerase-A hypersensitive protein 11


Mass: 68486.055 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P47112

Cellular component

Molecular function

Biological process

  • cell division (GO: 0051301)
  • double-strand break repair via break-induced replication (GO: 0000727)
  • pre-replicative complex assembly involved in nuclear cell cycle DNA replication (GO: 0006267)
  • regulation of DNA-dependent DNA replication initiation (GO: 0030174)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: Cdt1-Mcm2-7 / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae
Source (recombinant)Organism: Saccharomyces cerevisiae
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 22 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 63000 / Symmetry type: POINT

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