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Yorodumi- EMDB-6338: Cryo-EM study of the Eukaryotic Minichromosome Maintenance Complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6338 | |||||||||
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Title | Cryo-EM study of the Eukaryotic Minichromosome Maintenance Complex | |||||||||
Map data | Reconstruction of the Eukaryotic Minichromosome Maintenance Complex | |||||||||
Sample |
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Keywords | Cryo-EM / single particle / MCM2-7 / DNA replication | |||||||||
Function / homology | Function and homology information MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / nuclear DNA replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / Activation of the pre-replicative complex / CMG complex ...MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / MCM complex binding / nuclear DNA replication / premeiotic DNA replication / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / mitotic DNA replication / Activation of the pre-replicative complex / CMG complex / nuclear pre-replicative complex / MCM complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / replication fork protection complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / nuclear replication fork / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / DNA helicase activity / helicase activity / transcription elongation by RNA polymerase II / heterochromatin formation / single-stranded DNA binding / chromosome, telomeric region / DNA helicase / chromatin binding / DNA damage response / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Li N / Zhai Y / Zhang Y / Li W / Yang M / Lei J / Tye BK / Gao N | |||||||||
Citation | Journal: 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 / Abstract: DNA replication in eukaryotes is strictly regulated by several mechanisms. A central step in this replication is the assembly of the heterohexameric minichromosome maintenance (MCM2-7) helicase ...DNA replication in eukaryotes is strictly regulated by several mechanisms. A central step in this replication is the assembly of the heterohexameric minichromosome maintenance (MCM2-7) helicase complex at replication origins during G1 phase as an inactive double hexamer. Here, using cryo-electron microscopy, we report a near-atomic structure of the MCM2-7 double hexamer purified from yeast G1 chromatin. Our structure shows that two single hexamers, arranged in a tilted and twisted fashion through interdigitated amino-terminal domain interactions, form a kinked central channel. Four constricted rings consisting of conserved interior β-hairpins from the two single hexamers create a narrow passageway that tightly fits duplex DNA. This narrow passageway, reinforced by the offset of the two single hexamers at the double hexamer interface, is flanked by two pairs of gate-forming subunits, MCM2 and MCM5. These unusual features of the twisted and tilted single hexamers suggest a concerted mechanism for the melting of origin DNA that requires structural deformation of the intervening DNA. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6338.map.gz | 3.3 MB | EMDB map data format | |
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Header (meta data) | emd-6338-v30.xml emd-6338.xml | 8.8 KB 8.8 KB | Display Display | EMDB header |
Images | 400_6338.gif 80_6338.gif | 84.1 KB 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6338 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6338 | HTTPS FTP |
-Validation report
Summary document | emd_6338_validation.pdf.gz | 327 KB | Display | EMDB validaton report |
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Full document | emd_6338_full_validation.pdf.gz | 326.6 KB | Display | |
Data in XML | emd_6338_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6338 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6338 | HTTPS FTP |
-Related structure data
Related structure data | 3ja8MC 6eycM M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6338.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the Eukaryotic Minichromosome Maintenance Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Eukaryotic Minichromosome Maintenance Complex (MCM2-7)
Entire | Name: Eukaryotic Minichromosome Maintenance Complex (MCM2-7) |
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Components |
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-Supramolecule #1000: Eukaryotic Minichromosome Maintenance Complex (MCM2-7)
Supramolecule | Name: Eukaryotic Minichromosome Maintenance Complex (MCM2-7) type: sample / ID: 1000 / Oligomeric state: Double hexamer / Number unique components: 1 |
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Molecular weight | Theoretical: 1.2 MDa |
-Macromolecule #1: Eukaryotic Minichromosome Maintenance Complex
Macromolecule | Name: Eukaryotic Minichromosome Maintenance Complex / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: hexamer / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / synonym: Yeast / Location in cell: cytoplasm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50mM HEPES-KOH, 100mM K glutamate, 10mM Mg(OAc)2, 0.25% Triton X-100, 3mM ATP, 1mM EDTA |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Nov 25, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 4 µm / Number real images: 2230 / Average electron dose: 16 e/Å2 Details: Every image is the average of 14 frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: CTFFIND |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 85365 |