+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15123 | |||||||||
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Title | S. cerevisiae APC/C-Cdh1 complex | |||||||||
Map data | whole 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 / : / deactivation of mitotic spindle assembly checkpoint / ascospore wall assembly / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / ubiquitin-protein transferase activator activity / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process ...anaphase-promoting complex assembly / negative regulation of anaphase-promoting complex-dependent catabolic process / : / deactivation of mitotic spindle assembly checkpoint / ascospore wall assembly / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / ubiquitin-protein transferase activator activity / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / metaphase/anaphase transition of mitotic cell cycle / Antigen processing: Ubiquitination & Proteasome degradation / anaphase-promoting complex binding / positive regulation of ubiquitin protein ligase activity / exit from mitosis / protein K11-linked ubiquitination / positive regulation of protein autoubiquitination / reciprocal meiotic recombination / regulation of mitotic metaphase/anaphase transition / ubiquitin ligase inhibitor activity / mitotic sister chromatid segregation / cullin family protein binding / ligase activity / 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 / protein kinase activity / cell cycle / cell division / protein phosphorylation / ubiquitin protein ligase binding / mitochondrion / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Barford D / Vazquez-Fernandez 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 APC/C-Cdh1 complex Authors: Barford D / Vazquez-Fernandez 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_15123.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-15123-v30.xml emd-15123.xml | 41.2 KB 41.2 KB | Display Display | EMDB header |
Images | emd_15123.png | 101.2 KB | ||
Others | emd_15123_half_map_1.map.gz emd_15123_half_map_2.map.gz | 56.6 MB 55.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15123 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15123 | HTTPS FTP |
-Related structure data
Related structure data | 8a3tMC 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_15123.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | whole 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 map1
File | emd_15123_half_map_1.map | ||||||||||||
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Annotation | half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15123_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Anaphase promoting complex/cyclosome (APC/C) in complex with Cdh1...
+Supramolecule #1: Anaphase promoting complex/cyclosome (APC/C) in complex with Cdh1...
+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 DOC1
+Macromolecule #6: CDH1 isoform 1
+Macromolecule #7: HSL1 isoform 1
+Macromolecule #8: Anaphase-promoting complex subunit 1
+Macromolecule #9: Anaphase-promoting complex subunit 5
+Macromolecule #10: Anaphase-promoting complex subunit CDC23
+Macromolecule #11: Anaphase-promoting complex subunit SWM1
+Macromolecule #12: Anaphase-promoting complex subunit MND2
+Macromolecule #13: Anaphase-promoting complex subunit 4
+Macromolecule #14: Anaphase-promoting complex subunit 2
+Macromolecule #15: Anaphase-promoting complex subunit 11
+Macromolecule #16: ZINC ION
-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: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Pressure: 20.0 kPa | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 51.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 1 pixel / Digitization - Dimensions - Height: 1 pixel / Number grids imaged: 1 / Number real images: 12006 / Average exposure time: 2.0 sec. / Average electron dose: 59.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final 3D classification | Software - Name: RELION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 249193 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8a3t: |