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- PDB-5h7i: Cryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state -

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Basic information

Entry
Database: PDB / ID: 5h7i
TitleCryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state
Components
  • (DNA replication licensing factor ...) x 5
  • Cell division cycle protein CDT1Cell cycle
  • Minichromosome maintenance protein 5
KeywordsHYDROLASE / helicase / DNA replication
Function / homologyMCM6 C-terminal winged-helix domain / MCM N-terminal domain / MCM domain / AAA+ ATPase domain / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 ...MCM6 C-terminal winged-helix domain / MCM N-terminal domain / MCM domain / AAA+ ATPase domain / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Nucleic acid-binding, OB-fold / Mini-chromosome maintenance, conserved site / P-loop containing nucleoside triphosphate hydrolase / Mini-chromosome maintenance protein / MCM OB domain / MCM P-loop domain / Mini-chromosome maintenance protein 2 / MCM N-terminal domain / MCM OB domain / MCM family signature. / MCM family domain profile. / Orc1 removal from chromatin / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / MCM AAA-lid domain / MCM core complex / MCM complex binding / negative regulation of ATP-dependent DNA helicase activity / CMG complex / nuclear DNA replication / negative regulation of chromatin silencing at telomere / MCM complex / establishment of chromatin silencing / mitotic DNA replication initiation / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / DNA replication preinitiation complex / single-stranded DNA-dependent ATPase activity / double-strand break repair via break-induced replication / nuclear replication fork / replication fork protection complex / DNA strand elongation involved in DNA replication / chromatin silencing at silent mating-type cassette / DNA duplex unwinding / DNA unwinding involved in DNA replication / DNA helicase activity / DNA replication origin binding / DNA replication initiation / chromatin silencing at telomere / DNA helicase / helicase activity / chromosome, telomeric region / single-stranded DNA binding / nuclear chromosome, telomeric region / cell division / cellular response to DNA damage stimulus / chromatin binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / Cell division cycle protein CDT1 / DNA replication licensing factor MCM6
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 7.1 Å resolution
AuthorsZhai, Y. / Cheng, E. / Wu, H. / Li, N. / Yung, P.Y. / Gao, N. / Tye, B.K.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Open-ringed structure of the Cdt1-Mcm2-7 complex as a precursor of the MCM double hexamer.
Authors: Yuanliang Zhai / Erchao Cheng / Hao Wu / Ningning Li / Philip Yuk Kwong Yung / Ning Gao / Bik-Kwoon Tye
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 18, 2016 / Release: Feb 8, 2017
RevisionDateData content typeGroupProviderType
1.0Feb 8, 2017Structure modelrepositoryInitial release
1.1Feb 15, 2017Structure modelDatabase references
1.2Mar 15, 2017Structure modelDatabase references

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Structure visualization

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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)674,8557
Polyers674,8557
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: Protein/peptide 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) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM2, YBL023C, YBL0438 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P29469, DNA helicase
#2: Protein/peptide DNA replication licensing factor MCM3 / Minichromosome maintenance protein 3


Mass: 107653.508 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM3, YEL032W, SYGP-ORF23 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P24279, DNA helicase
#3: Protein/peptide 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) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM4, CDC54, HCD21, YPR019W, YP9531.13 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P30665, DNA helicase
#5: Protein/peptide 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) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM6, YGL201C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P53091, DNA helicase
#6: Protein/peptide 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) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM7, CDC47, YBR202W, YBR1441 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38132, DNA helicase

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Protein/peptide , 2 types, 2 molecules 5C

#4: Protein/peptide 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) (yeast)
Strain: ATCC 204508 / S288c / Gene: MCM5, CDC46, YLR274W, L9328.1 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P29496, DNA helicase
#7: Protein/peptide Cell division cycle protein CDT1 / Cell cycle / 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) (yeast)
Strain: ATCC 204508 / S288c / Gene: TAH11, CDT1, SID2, YJR046W, J1641 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P47112

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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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 (baker's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast) / Plasmid: yJF38
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 FIELDBright-field microscopy
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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