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- EMDB-6338: Cryo-EM study of the Eukaryotic Minichromosome Maintenance Complex -

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Entry
Database: EMDB / ID: 6338
TitleCryo-EM study of the Eukaryotic Minichromosome Maintenance Complex
Map dataReconstruction of the Eukaryotic Minichromosome Maintenance Complex
SampleEukaryotic Minichromosome Maintenance Complex (MCM2-7)
  • Eukaryotic Minichromosome Maintenance Complex
KeywordsCryo-EM / single particle / MCM2-7 / DNA replication
Function / homologyP-loop containing nucleoside triphosphate hydrolase / Mini-chromosome maintenance protein / MCM domain / MCM OB 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 ...P-loop containing nucleoside triphosphate hydrolase / Mini-chromosome maintenance protein / MCM domain / MCM OB 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 / MCM P-loop domain / DNA replication licensing factor Mcm7 / Mini-chromosome maintenance protein 2 / MCM N-terminal domain / MCM OB domain / MCM family signature. / MCM family domain profile. / Nucleic acid-binding, OB-fold / Orc1 removal from chromatin / Mini-chromosome maintenance, conserved site / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / MCM N-terminal domain / MCM complex binding / negative regulation of ATP-dependent DNA helicase activity / MCM core complex / 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 / DNA strand elongation involved in DNA replication / replication fork protection complex / chromatin silencing at silent mating-type cassette / DNA duplex unwinding / DNA helicase activity / DNA unwinding involved in DNA replication / chromatin silencing at telomere / DNA replication origin binding / DNA replication initiation / DNA helicase / helicase activity / chromosome, telomeric region / single-stranded DNA binding / nuclear chromosome, telomeric region / 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 / DNA replication licensing factor MCM6
Function and homology information
SourceSaccharomyces cerevisiae S288c (Yeast)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsLi N / Zhai Y / Zhang Y / Li W / Yang M / Lei J / Tye BK / Gao N
CitationJournal: Nature / Year: 2015
Title: Structure of the eukaryotic MCM complex at 3.8 Å.
Authors: Ningning Li / Yuanliang Zhai / Yixiao Zhang / Wanqiu Li / Maojun Yang / Jianlin Lei / Bik-Kwoon Tye / Ning Gao
Validation ReportPDB-ID: 3ja8

SummaryFull report
PDB-ID: 6eyc

SummaryFull report
About validation report
DateDeposition: May 9, 2015 / Header (metadata) release: Jul 15, 2015 / Map release: Aug 5, 2015 / Last update: Aug 19, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3ja8
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-3ja8
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6eyc
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-3ja8
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6eyc
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6338.map.gz (map file in CCP4 format, 105470 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.32 Å/pix.
= 396. Å
300 pix
1.32 Å/pix.
= 396. Å
300 pix
1.32 Å/pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:5 (by author), 5 (movie #1):
Minimum - Maximum-16.13556290 - 32.02772141
Average (Standard dev.)-0.05845978 (0.69713837)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 396.00003 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z396.000396.000396.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-16.13632.028-0.058

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Supplemental data

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Sample components

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Entire Eukaryotic Minichromosome Maintenance Complex (MCM2-7)

EntireName: Eukaryotic Minichromosome Maintenance Complex (MCM2-7)
Number of components: 1 / Oligomeric State: Double hexamer
MassTheoretical: 1.2 MDa

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Component #1: protein, Eukaryotic Minichromosome Maintenance Complex

ProteinName: Eukaryotic Minichromosome Maintenance Complex / Oligomeric Details: hexamer / Recombinant expression: No / Number of Copies: 2
SourceSpecies: Saccharomyces cerevisiae S288c (Yeast)
Source (natural)Location in cell: cytoplasm

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 50mM HEPES-KOH, 100mM K glutamate, 10mM Mg(OAc)2, 0.25% Triton X-100, 3mM ATP, 1mM EDTA
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Nov 25, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2230 / Sampling size: 4 microns
Details: Every image is the average of 14 frames recorded by the direct electron detector

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 85365
3D reconstructionSoftware: RELION / CTF correction: CTFFIND / Resolution: 3.8 Å / Resolution method: FSC 0.143, gold-standard

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