+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1254 | |||||||||
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Title | Hexameric ring structure of human MCM10 DNA replication factor. | |||||||||
Map data | Surface views of human Mcm10 top side bottom stereo | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 16.0 Å | |||||||||
Authors | Okorokov AL / Orlova EV | |||||||||
Citation | Journal: EMBO Rep / Year: 2007 Title: Hexameric ring structure of human MCM10 DNA replication factor. Authors: Andrei L Okorokov / Alastair Waugh / Julie Hodgkinson / Andal Murthy / Hye Kyung Hong / Elisabetta Leo / Michael B Sherman / Kai Stoeber / Elena V Orlova / Gareth H Williams / Abstract: The DNA replication factor minichromosome maintenance 10 (MCM10) is a conserved, abundant nuclear protein crucial for origin firing. During the transition from pre-replicative complexes to pre- ...The DNA replication factor minichromosome maintenance 10 (MCM10) is a conserved, abundant nuclear protein crucial for origin firing. During the transition from pre-replicative complexes to pre-initiation complexes, MCM10 recruitment to replication origins is required to provide a physical link between the MCM2-7 complex DNA helicase and DNA polymerases. Here, we report the molecular structure of human MCM10 as determined by electron microscopy and single-particle analysis. The MCM10 molecule is a ring-shaped hexamer with large central and smaller lateral channels and a system of inner chambers. This structure, together with biochemical data, suggests that this important protein uses its architecture to provide a docking module for assembly of the molecular machinery required for eukaryotic DNA replication. | |||||||||
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_1254.map.gz | 1.4 MB | EMDB map data format | |
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Header (meta data) | emd-1254-v30.xml emd-1254.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
Images | 1254.gif | 64.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1254 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1254 | HTTPS FTP |
-Validation report
Summary document | emd_1254_validation.pdf.gz | 229.8 KB | Display | EMDB validaton report |
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Full document | emd_1254_full_validation.pdf.gz | 228.9 KB | Display | |
Data in XML | emd_1254_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1254 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1254 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1254.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Surface views of human Mcm10 top side bottom stereo | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.59 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 : recombinant human Mcm10
Entire | Name: recombinant human Mcm10 |
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Components |
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-Supramolecule #1000: recombinant human Mcm10
Supramolecule | Name: recombinant human Mcm10 / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: homohexamer / Number unique components: 1 |
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Molecular weight | Experimental: 650 KDa / Theoretical: 590 KDa / Method: size-exclusion FPLC |
-Macromolecule #1: Mcm10
Macromolecule | Name: Mcm10 / type: protein_or_peptide / ID: 1 / Name.synonym: DNA replication factor / Details: UniProtKB/TrEMBL entry Q3MIR3 / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Location in cell: nuclear |
Molecular weight | Experimental: 590 KDa / Theoretical: 650 KDa |
Recombinant expression | Organism: Escherichia coli, Rosetta / Recombinant plasmid: pProEX-HT-B |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.01 mg/mL |
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Buffer | pH: 6.8 Details: 25 mM Tris-HCl pH 9.0, 150 mM NaCl, 10 mM MgCl2, 50 mM KCl |
Staining | Type: NEGATIVE Details: Grids were stained with 2% w/v methylamine tungstate, (Nano-W, Nanoprobes Inc.) for 1 min. |
Grid | Details: 400 mesh, freshly glow-discharged in air |
Vitrification | Cryogen name: NONE |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Details | images were taken on FEI Technai T10 microscope in low dose mode. |
Date | Jan 1, 2005 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 15 / Average electron dose: 15 e/Å2 / Camera length: 500 / Od range: 1.4 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 44000 |
Sample stage | Specimen holder: eucentric / Specimen holder model: OTHER |
-Image processing
Details | The particles were selected interactively at the computer terminal. close |
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CTF correction | Details: each particle |
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Details: Final map was calculated from 197 best classes / Number images used: 5000 |
Final two d classification | Number classes: 197 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID - 0: 1 / Chain - Chain ID - 1: L / Chain - Chain ID - 2: T / Chain - Chain ID - 3: L |
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Software | Name: URO |
Details | Protocol: rigid body. The domains were fitted automatically using URO |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: correlation coeficient |