+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38111 | |||||||||
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Title | MCM in complex with dsDNA in presence of ATP. | |||||||||
Map data | MCM_ATP_dsDNA | |||||||||
Sample |
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Keywords | Helicase / Replication / HYDROLASE | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 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 complex with dsDNA in presence of ATP 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_38111.map.gz | 11 MB | EMDB map data format | |
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Header (meta data) | emd-38111-v30.xml emd-38111.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_38111.png | 53.5 KB | ||
Filedesc metadata | emd-38111.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38111 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38111 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38111.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | MCM_ATP_dsDNA | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.932 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : MCM homohexamer in complex with dsDNA in presence of ATP
Entire | Name: MCM homohexamer in complex with dsDNA in presence of ATP |
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Components |
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-Supramolecule #1: MCM homohexamer in complex with dsDNA in presence of ATP
Supramolecule | Name: MCM homohexamer in complex with dsDNA in presence of ATP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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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 |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-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: FEI FALCON IV (4k x 4k) / Average electron dose: 39.0 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: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126808 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |