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- PDB-5bk4: Cryo-EM structure of Mcm2-7 double hexamer on dsDNA -

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Entry
Database: PDB / ID: 5bk4
TitleCryo-EM structure of Mcm2-7 double hexamer on dsDNA
DescriptorMinichromosome maintenance protein 5
(DNA replication licensing factor ...) x 5
KeywordsHYDROLASE/DNA / complex / DNA replication / HYDROLASE-DNA complex
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (3.9 Å resolution / Particle / Single particle)
AuthorsLi, H. / Yuan, Z. / Bai, L.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, E9529-E9538

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E9529-E9538 Yorodumi Papers
Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model.
Yasunori Noguchi / Zuanning Yuan / Lin Bai / Sarah Schneider / Gongpu Zhao / Bruce Stillman / Christian Speck / Huilin Li

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 12, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 8, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Nov 22, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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: DNA replication licensing factor MCM5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
A: DNA replication licensing factor MCM2
B: DNA replication licensing factor MCM3
C: DNA replication licensing factor MCM4
D: DNA replication licensing factor MCM5
E: DNA replication licensing factor MCM6
F: DNA replication licensing factor MCM7
S: DNA (60-mer), strand 1
O: DNA (60-mer), strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,253,14022
Polyers1,249,72214
Non-polymers3,4188
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)115650
ΔGint (kcal/M)-582
Surface area (Å2)387600

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Components

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DNA replication licensing factor ... , 6 types, 12 molecules 2A3B4C5D6E7F

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


Mass: 98911.539 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P29469, EC: 3.6.4.12
#2: Polypeptide(L)DNA replication licensing factor MCM3 / Minichromosome maintenance protein 3


Mass: 107653.508 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P24279, EC: 3.6.4.12
#3: Polypeptide(L)DNA replication licensing factor MCM4 / Cell division control protein 54


Mass: 105138.375 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P30665, EC: 3.6.4.12
#4: Polypeptide(L)DNA replication licensing factor MCM5 / Minichromosome maintenance protein 5 / Cell division control protein 46


Mass: 86505.734 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P29496, EC: 3.6.4.12
#5: Polypeptide(L)DNA replication licensing factor MCM6 / Minichromosome maintenance protein 6


Mass: 113110.211 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P53091, EC: 3.6.4.12
#6: Polypeptide(L)DNA replication licensing factor MCM7 / Cell division control protein 47 / Minichromosome maintenance protein 7


Mass: 95049.875 Da / Num. of mol.: 2 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P38132, EC: 3.6.4.12

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DNA (60-mer), strand ... , 2 types, 2 molecules SO

#7: DNA chainDNA (60-mer), strand 1


Mass: 18491.848 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae
#8: DNA chainDNA (60-mer), strand 2


Mass: 18491.848 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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Non-polymers , 1 types, 8 molecules

#9: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 8 / Formula: C10H15N5O10P2

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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

Component
IDNameTypeEntity IDParent IDSource
1Mcm double hexamer bound to double-stranded DNACOMPLEX1,2,3,4,5,6,7,80MULTIPLE SOURCES
2Mcm double hexamerCOMPLEX1,2,3,4,5,61RECOMBINANT
3synthetic double-stranded DNACOMPLEX7,81NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
114932Saccharomyces cerevisiae
224932Saccharomyces cerevisiae
334932Saccharomyces cerevisiae
Source (recombinant)Organism: Saccharomyces cerevisiae
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 10 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1RELION2PARTICLE SELECTION1
2RELION1.4PARTICLE SELECTION1
3RELION2.0IMAGE ACQUISITION1
4RELION1.4IMAGE ACQUISITION1
6CTFFIND4CTF CORRECTION1
7GctfCTF CORRECTION1
10chimera1.11MODEL FITTING1
11Coot0.8MODEL FITTING1
13PHENIX1.11MODEL REFINEMENT1
14RELION2INITIAL EULER ASSIGNMENT1
15RELION2FINAL EULER ASSIGNMENT1
17RELION2RECONSTRUCTION1
CTF correctionType: NONE
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 58772 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00863728
ELECTRON MICROSCOPYf_angle_d1.21586740
ELECTRON MICROSCOPYf_dihedral_angle_d14.06838738
ELECTRON MICROSCOPYf_chiral_restr0.06310082
ELECTRON MICROSCOPYf_plane_restr0.00710746

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