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Yorodumi- EMDB-2925: Cryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex. -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2925 | |||||||||
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Title | Cryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex. | |||||||||
Map data | Cryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex. | |||||||||
Sample |
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Keywords | Ubiquitination / Cell cycle. | |||||||||
Function / homology | Function and homology information negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint ...negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / free ubiquitin chain polymerization / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of synaptic plasticity / regulation of exit from mitosis / anaphase-promoting complex binding / Phosphorylation of the APC/C / ubiquitin ligase activator activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / positive regulation of ubiquitin-dependent protein catabolic process / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / exit from mitosis / mitotic metaphase chromosome alignment / E2 ubiquitin-conjugating enzyme / ubiquitin-like protein ligase binding / ubiquitin conjugating enzyme activity / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / Antigen processing: Ubiquitination & Proteasome degradation / Transcriptional Regulation by VENTX / positive regulation of axon extension / heterochromatin / protein K48-linked ubiquitination / ubiquitin ligase complex / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / cyclin binding / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / nuclear periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / brain development / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / kinetochore / spindle / protein polyubiquitination / positive regulation of protein catabolic process / Separation of Sister Chromatids / ubiquitin-protein transferase activity / microtubule cytoskeleton / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / mitotic cell cycle / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / molecular adaptor activity / cell differentiation / protein ubiquitination / cell cycle / cell division / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / nucleolus / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
Authors | Chang L / Zhang Z / Yang J / McLaughlin SH / Barford D | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Atomic structure of the APC/C and its mechanism of protein ubiquitination. Authors: Leifu Chang / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / David Barford / Abstract: The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the ...The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the mitotic checkpoint complex and interphase early mitotic inhibitor 1 (Emi1) ensures the correct order and timing of distinct cell-cycle transitions. Here we use cryo-electron microscopy to determine atomic structures of APC/C-coactivator complexes with either Emi1 or a UbcH10-ubiquitin conjugate. These structures define the architecture of all APC/C subunits, the position of the catalytic module and explain how Emi1 mediates inhibition of the two E2s UbcH10 and Ube2S. Definition of Cdh1 interactions with the APC/C indicates how they are antagonized by Cdh1 phosphorylation. The structure of the APC/C with UbcH10-ubiquitin reveals insights into the initiating ubiquitination reaction. Our results provide a quantitative framework for the design of future experiments to investigate APC/C functions in vivo. | |||||||||
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_2925.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-2925-v30.xml emd-2925.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
Images | emd_2925.jpg | 118.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2925 | HTTPS FTP |
-Validation report
Summary document | emd_2925_validation.pdf.gz | 221.2 KB | Display | EMDB validaton report |
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Full document | emd_2925_full_validation.pdf.gz | 220.3 KB | Display | |
Data in XML | emd_2925_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2925 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2925 | HTTPS FTP |
-Related structure data
Related structure data | 5a31MC 2924C 2926C 4ui9C 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_2925.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.77 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 APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex
+Supramolecule #1000: Recombinant human APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex
+Macromolecule #1: Apc1
+Macromolecule #2: Apc2
+Macromolecule #3: Apc3
+Macromolecule #4: Apc4
+Macromolecule #5: Apc5
+Macromolecule #6: Apc6
+Macromolecule #7: Apc7
+Macromolecule #8: Apc8
+Macromolecule #9: Apc10
+Macromolecule #10: Apc11
+Macromolecule #11: Apc12
+Macromolecule #12: Apc13
+Macromolecule #13: Apc15
+Macromolecule #14: Apc16
+Macromolecule #15: Cdh1
+Macromolecule #16: Hsl1
+Macromolecule #17: E2-ubiquitin conjugate
+Macromolecule #18: UbcH10-ubiquitin
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 8 / Details: 20 mM HEPES, 150 mM NaCl, 1 mM DTT |
Grid | Details: R2/2 Quantifoil grid with thin carbon support. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 5 seconds before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Date | Jul 12, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 16 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using an automatic selection program |
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CTF correction | Details: Each micrograph |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 19939 |