+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0823 | |||||||||
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Title | Cryo-EM map of human MCM8/9 complex | |||||||||
Map data | Use lower contour value for C terminal display | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.1 Å | |||||||||
Authors | Li J / Yu D / Liu L / Zeng H / Hu Z / Xu H / Liu B / Liang H / Ouyang Q / Liu Y | |||||||||
Citation | Journal: Structure / Year: 2021 Title: Structural study of the N-terminal domain of human MCM8/9 complex. Authors: Jun Li / Daqi Yu / Lan Liu / Huanhuan Liang / Qi Ouyang / Yingfang Liu / Abstract: MCM8/9 is a complex involved in homologous recombination (HR) repair pathway. MCM8/9 dysfunction can cause genome instability and result in primary ovarian insufficiency (POI). However, the mechanism ...MCM8/9 is a complex involved in homologous recombination (HR) repair pathway. MCM8/9 dysfunction can cause genome instability and result in primary ovarian insufficiency (POI). However, the mechanism underlying these effects is largely unknown. Here, we report crystal structures of the N-terminal domains (NTDs) of MCM8 and MCM9, and build a ring-shaped NTD structure based on a 6.6 Å resolution cryoelectron microscopy map. This shows that the MCM8/9 complex forms a 3:3 heterohexamer in an alternating pattern. A positively charged DNA binding channel and a putative ssDNA exit pathway for fork DNA unwinding are revealed. Based on the atomic model, the potential effects of the clinical POI mutants are interpreted. Surprisingly, the zinc-finger motifs are found to be capable of binding an iron atom as well. Overall, our results provide a model for the formation of the MCM8/9 complex and provide a path for further studies. | |||||||||
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_0823.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-0823-v30.xml emd-0823.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0823_fsc.xml | 5.9 KB | Display | FSC data file |
Images | emd_0823.png | 200.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0823 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0823 | HTTPS FTP |
-Validation report
Summary document | emd_0823_validation.pdf.gz | 348.5 KB | Display | EMDB validaton report |
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Full document | emd_0823_full_validation.pdf.gz | 348.1 KB | Display | |
Data in XML | emd_0823_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | emd_0823_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0823 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0823 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0823.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Use lower contour value for C terminal display | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 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 : Minichromosome Maintenance (MCM) 8/9 Complex
Entire | Name: Minichromosome Maintenance (MCM) 8/9 Complex |
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Components |
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-Supramolecule #1: Minichromosome Maintenance (MCM) 8/9 Complex
Supramolecule | Name: Minichromosome Maintenance (MCM) 8/9 Complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 500 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||
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Buffer | pH: 7.8 / Component:
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Grid | Model: C-flat-1.2/1.3 4C / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE | ||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 7420 pixel / Digitization - Dimensions - Height: 7676 pixel / Digitization - Frames/image: 1-40 / Number real images: 3711 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 36496 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |