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- PDB-6f0l: S. cerevisiae MCM double hexamer bound to duplex DNA -

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Basic information

Entry
Database: PDB / ID: 6f0l
TitleS. cerevisiae MCM double hexamer bound to duplex DNA
DescriptorMinichromosome maintenance protein 5
(DNA replication licensing factor ...) x 5
KeywordsHYDROLASE / AAA+ Helicase / Nucleoprotein complex / DNA replication / Double hexamer
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
Synthetic construct
MethodElectron microscopy (4.77 Å resolution / Particle / Single particle)
AuthorsAbid Ali, F. / Pye, V.E. / Douglas, M.E. / Locke, J. / Nans, A. / Diffley, J.F.X. / Costa, A.
Citationto be published

to be published Search PubMed
Cryo-EM structure of a licensed DNA replication origin
Abid Ali, F. / Douglas, M.E. / Locke, J. / Pye, V.E. / Nans, A. / Diffley, J.F.X. / Costa, A.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2017 / Release: Dec 6, 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
A: DNA replication licensing factor MCM2
B: DNA replication licensing factor MCM3
C: DNA replication licensing factor MCM4
D: Minichromosome maintenance protein 5
E: DNA replication licensing factor MCM6
F: DNA replication licensing factor MCM7
X: DNA (62-MER)
Y: DNA (62-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,252,66718
Polyers1,250,95814
Non-polymers1,7094
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)112000
ΔGint (kcal/M)-528
Surface area (Å2)394180
MethodPISA

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Components

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DNA replication licensing factor ... , 5 types, 10 molecules 2A3B4C6E7F

#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 (strain ATCC 204508 / S288c)
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 (strain ATCC 204508 / S288c)
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 (strain ATCC 204508 / S288c)
References: UniProt: P30665, 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 (strain ATCC 204508 / S288c)
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 (strain ATCC 204508 / S288c)
References: UniProt: P38132, EC: 3.6.4.12

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DNA chain , 2 types, 2 molecules XY

#7: DNA chainDNA (62-MER)


Mass: 19094.236 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#8: DNA chainDNA (62-MER)


Mass: 19125.244 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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Polypeptide(L) / Non-polymers , 2 types, 6 molecules 5D

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


Mass: 86505.734 Da / Num. of mol.: 2
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P29496, EC: 3.6.4.12
#9: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 4 / 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

ComponentName: S. cerevisiae MCM double hexamer bound to DNA / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8 / Source: RECOMBINANT
Molecular weightValue: 1.2 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae
Source (recombinant)Organism: Saccharomyces cerevisiae
Buffer solutionpH: 7.6
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: 1.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1EMAN2.07PARTICLE SELECTION1
2EPUIMAGE ACQUISITION1
4GctfCTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
9cryoSPARCINITIAL EULER ASSIGNMENT1
10cryoSPARCFINAL EULER ASSIGNMENT1
13PHENIXMODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2
3D reconstructionResolution: 4.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 52319 / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL

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