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Yorodumi- PDB-8pkp: Cryo-EM structure of the apo Anaphase-promoting complex/cyclosome... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pkp | |||||||||
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Title | Cryo-EM structure of the apo Anaphase-promoting complex/cyclosome (APC/C) at 3.2 Angstrom resolution | |||||||||
Components |
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Keywords | CELL CYCLE / APC/C / cyclosome / Cdc20 / Cdh1 / ubiquitination / Emi1 / mitosis | |||||||||
Function / homology | Function and homology information 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 ...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 / positive regulation of synaptic plasticity / regulation of exit from mitosis / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / ubiquitin-ubiquitin ligase activity / mitotic metaphase chromosome alignment / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / positive regulation of axon extension / protein K48-linked ubiquitination / heterochromatin / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / 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 / Separation of Sister Chromatids / ubiquitin-protein transferase activity / microtubule cytoskeleton / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / molecular adaptor activity / cell differentiation / protein ubiquitination / cell division / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / nucleolus / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Hoefler, A. / Yu, J. / Chang, L. / Zhang, Z. / Yang, J. / Boland, A. / Barford, D. | |||||||||
Funding support | Switzerland, United Kingdom, 2items
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Citation | Journal: To Be Published Title: High-resolution structure of the Anaphase-promoting complex (APC/C) bound to co-activator Cdh1 Authors: Hoefler, A. / Yu, J. / Chang, L. / Zhang, Z. / Yang, J. / Boland, A. / Barford, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pkp.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8pkp.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8pkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/8pkp ftp://data.pdbj.org/pub/pdb/validation_reports/pk/8pkp | HTTPS FTP |
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-Related structure data
Related structure data | 17751MC 51190 7qe7C 9gawC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Anaphase-promoting complex subunit ... , 11 types, 13 molecules ADGWHLMOYZINC
#1: Protein | Mass: 216725.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC1, TSG24 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H1A4 | ||||||||||||||||
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#2: Protein | Mass: 14286.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC15, C11orf51, HSPC020 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60006 | ||||||||||||||||
#3: Protein | Mass: 9793.999 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC26, ANAPC12, C9orf17 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NHZ8 #4: Protein | | Mass: 11677.995 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC16, C10orf104, CENP-27 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96DE5 #7: Protein | | Mass: 21282.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC10, APC10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UM13 #8: Protein | | Mass: 8528.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC13 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BS18 #9: Protein | | Mass: 85179.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC5, APC5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX4 #11: Protein | Mass: 63204.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC7, APC7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX3 #12: Protein | | Mass: 93014.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC4, APC4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX5 #13: Protein | | Mass: 93938.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC2, APC2, KIAA1406 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX6 #14: Protein | | Mass: 9854.647 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC11, HSPC214 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NYG5 |
-Cell division cycle protein ... , 3 types, 6 molecules JPKQUV
#5: Protein | Mass: 91973.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC27, ANAPC3, D0S1430E, D17S978E / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30260 #6: Protein | Mass: 71747.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC16, ANAPC6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13042 #10: Protein | Mass: 68921.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC23, ANAPC8 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJX2 |
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-Non-polymers , 1 types, 4 molecules
#15: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Apo Anaphase-promoting complex (APC/C) / Type: COMPLEX / Entity ID: #1-#14 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 1.2 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 8297 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1800000 / Details: The particles were automatically selected | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174356 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 82 / Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5G05 Accession code: 5G05 / Source name: PDB / Type: experimental model |