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- EMDB-38109: MCM in the Apo state. -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38109
TitleMCM in the Apo state.
Map dataSample of MCM_apo
Sample
  • Complex: MCM homohexamer
    • Protein or peptide: mini-chromosome maintenance complex 3
KeywordsHelicase / Replication / HYDROLASE
Biological speciesThermococcus kodakarensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMa J / Yi G / Ye M / MacGregor-Chatwin C / Sheng Y / Lu Y / Li M / Gilbert RJC / Zhang P
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: MCM in the Apo state
Authors: Ma J / Yi G / Ye M / MacGregor-Chatwin C / Sheng Y / Lu Y / Li M / Gilbert RJC / Zhang P
History
DepositionNov 25, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38109.png

Downloads & links

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Map

FileDownload / File: emd_38109.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSample of MCM_apo
Voxel sizeX=Y=Z: 1.072 Å
Density
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.1200522 - 1.7625575
Average (Standard dev.)0.0017246403 (±0.020496562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 411.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : MCM homohexamer

EntireName: MCM homohexamer
Components
  • Complex: MCM homohexamer
    • Protein or peptide: mini-chromosome maintenance complex 3

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Supramolecule #1: MCM homohexamer

SupramoleculeName: MCM homohexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermococcus kodakarensis (archaea)

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Macromolecule #1: mini-chromosome maintenance complex 3

MacromoleculeName: mini-chromosome maintenance complex 3 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Molecular weightTheoretical: 76.631242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDREEMIARF AKFLREYVDD EGNEVYINRL KDLLTVTPKR SLAIDWAHLN SFDPELADEL LNNPEEAIAS AEDAIQIVLR EPPLLVERE FKVHARFYNL PKTLLVKELG SEHINKLIQV EGIITRVSEV KPFVEKAVFV CRDCGNEMVR LQRPYENLVK P AKCDACGS ...String:
MDREEMIARF AKFLREYVDD EGNEVYINRL KDLLTVTPKR SLAIDWAHLN SFDPELADEL LNNPEEAIAS AEDAIQIVLR EPPLLVERE FKVHARFYNL PKTLLVKELG SEHINKLIQV EGIITRVSEV KPFVEKAVFV CRDCGNEMVR LQRPYENLVK P AKCDACGS RNIELDVDKS RFLNFQSFRL QDRPESLKGG QMPRFVDAIL LDDLVDAALP GDRVLVTGVL RVILEQREKR PI FKKILEV NHIEQLSKEI EELEISPEDE QKIRELAKRK DIVDAIVDSI APAIWGHRIV KKGIALALFG GVQRTLPDGT KLR GESHVL LVGDPGVAKS QLLRYVANLA PRAIYTSGKS SSAAGLTAAA VRDEFTGSWV LEAGVLVLAD GGFALIDEFD KMSD RDRSA IHEALEQQTI SISKAGITAT LNSRTTVIAA ANPKFGRFNR HKSLPEQLDL PPTLLSRFDL IFLLLDEPDE KVDAS IAEH ILKVRRGEAE AVTPKIPYDL LKKYIAYARK NVHPVLSREA MEEIKRYYVK MRKGLRRGDE DGVQPIPITA RQLEAL IRL SEAHARMRLS ETVTREDARA AIEIIEAMMK TIAVDEEGNL DVSILEVGKS SKKINKIEKL VDIIKSLESE GEFGAPE EK VIEAAKQAGI GTKADIEKLL NELKSDGRVY EPRAGFYRVI

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Generated using ab-initio reconstruction routine in cryoSPARC
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 445096

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