+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38109 | |||||||||
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Title | MCM in the Apo state. | |||||||||
Map data | Sample of MCM_apo | |||||||||
Sample |
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Keywords | Helicase / Replication / HYDROLASE | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.26 Å | |||||||||
Authors | Ma J / Yi G / Ye M / MacGregor-Chatwin C / Sheng Y / Lu Y / Li M / Gilbert RJC / Zhang P | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38109.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-38109-v30.xml emd-38109.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | emd_38109.png | 70.3 KB | ||
Filedesc metadata | emd-38109.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38109 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38109 | HTTPS FTP |
-Validation report
Summary document | emd_38109_validation.pdf.gz | 358.3 KB | Display | EMDB validaton report |
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Full document | emd_38109_full_validation.pdf.gz | 357.9 KB | Display | |
Data in XML | emd_38109_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_38109_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38109 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38109 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38109.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sample of MCM_apo | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.072 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : MCM homohexamer
Entire | Name: MCM homohexamer |
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Components |
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-Supramolecule #1: MCM homohexamer
Supramolecule | Name: MCM homohexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermococcus kodakarensis (archaea) |
-Macromolecule #1: mini-chromosome maintenance complex 3
Macromolecule | Name: mini-chromosome maintenance complex 3 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermococcus kodakarensis (archaea) |
Molecular weight | Theoretical: 76.631242 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: Generated using ab-initio reconstruction routine in cryoSPARC |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 445096 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |