+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15201 | |||||||||
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Title | S. cerevisiae apo phosphorylated APC/C | |||||||||
Map data | EM map | |||||||||
Sample |
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Function / homology | Function and homology information anaphase-promoting complex assembly / negative regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / ascospore wall assembly / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / anaphase-promoting complex / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process ...anaphase-promoting complex assembly / negative regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / ascospore wall assembly / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / anaphase-promoting complex / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / protein K11-linked ubiquitination / positive regulation of protein autoubiquitination / reciprocal meiotic recombination / regulation of mitotic metaphase/anaphase transition / exit from mitosis / ligase activity / mitotic sister chromatid segregation / ubiquitin ligase inhibitor activity / cullin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / enzyme regulator activity / negative regulation of DNA-templated DNA replication initiation / regulation of mitotic cell cycle / cyclin binding / nuclear periphery / kinetochore / spindle pole / ubiquitin protein ligase activity / chromatin organization / ubiquitin-dependent protein catabolic process / molecular adaptor activity / protein ubiquitination / cell cycle / cell division / ubiquitin protein ligase binding / mitochondrion / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Barford D / Fernandez-Vazquez E / Zhang Z / Yang J | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the S. cerevisiae apo phosphorylated APC/C Authors: Barford D / Fernandez-Vazquez E / Zhang Z / Yang J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15201.map.gz | 6.2 MB | EMDB map data format | |
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Header (meta data) | emd-15201-v30.xml emd-15201.xml | 37.7 KB 37.7 KB | Display Display | EMDB header |
Images | emd_15201.png | 90.9 KB | ||
Others | emd_15201_half_map_1.map.gz emd_15201_half_map_2.map.gz | 57.1 MB 57.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15201 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15201 | HTTPS FTP |
-Validation report
Summary document | emd_15201_validation.pdf.gz | 537.4 KB | Display | EMDB validaton report |
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Full document | emd_15201_full_validation.pdf.gz | 537 KB | Display | |
Data in XML | emd_15201_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_15201_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15201 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15201 | HTTPS FTP |
-Related structure data
Related structure data | 8a61MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15201.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EM map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.38 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map2
File | emd_15201_half_map_1.map | ||||||||||||
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Annotation | Half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map1
File | emd_15201_half_map_2.map | ||||||||||||
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Annotation | Half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Phosphorylated apo anaphase promoting complex/cyclosome (APC/C)
+Supramolecule #1: Phosphorylated apo anaphase promoting complex/cyclosome (APC/C)
+Macromolecule #1: Anaphase-promoting complex subunit CDC27
+Macromolecule #2: Anaphase-promoting complex subunit CDC16
+Macromolecule #3: Anaphase-promoting complex subunit CDC26
+Macromolecule #4: Anaphase-promoting complex subunit 9
+Macromolecule #5: Anaphase-promoting complex subunit 2
+Macromolecule #6: Anaphase-promoting complex subunit 11
+Macromolecule #7: Anaphase-promoting complex subunit 1
+Macromolecule #8: Anaphase-promoting complex subunit 5
+Macromolecule #9: Anaphase-promoting complex subunit CDC23
+Macromolecule #10: Anaphase-promoting complex subunit SWM1
+Macromolecule #11: Anaphase-promoting complex subunit MND2
+Macromolecule #12: Anaphase-promoting complex subunit 4
+Macromolecule #13: Anaphase-promoting complex subunit DOC1
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
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Buffer | pH: 8.3 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting 2 secs. |
-Electron microscopy
Microscope | TFS KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 1034 pixel / Digitization - Dimensions - Height: 1034 pixel / Digitization - Sampling interval: 1.7 µm / Number grids imaged: 1 / Number real images: 5904 / Average exposure time: 2.0 sec. / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 51.0 µm / Calibrated defocus max: 3.9 µm / Calibrated defocus min: 2.6 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8a61: |