+Open data
-Basic information
Entry | Database: PDB / ID: 8a3t | |||||||||
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Title | S. cerevisiae APC/C-Cdh1 complex | |||||||||
Components |
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Keywords | CELL CYCLE / APC/C / ubiqutiniation / D-box / Cdh1 | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Barford, D. / Vazquez-Fernandez, E. / Zhang, Z. / Yang, J. | |||||||||
Funding support | United Kingdom, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a3t.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8a3t.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 8a3t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/8a3t ftp://data.pdbj.org/pub/pdb/validation_reports/a3/8a3t | HTTPS FTP |
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-Related structure data
Related structure data | 15123MC M: map data used to model this data C: citing same article (ref.) |
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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 ... , 13 types, 17 molecules FHJKGWEACODPINQTU
#1: Protein | Mass: 85487.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CDC27, APC3, SNB1, YBL084C, YBL0718 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38042 #2: Protein | Mass: 96282.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CDC16, YKL022C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P09798 #3: Protein | Mass: 14096.860 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CDC26, HIT3, SCD26, YFR036W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14724 #4: Protein | | Mass: 30901.439 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: APC9, YLR102C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12107 #5: Protein | | Mass: 28810.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: DOC1, APC10, YGL240W, HRC283 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53068 #8: Protein | | Mass: 196372.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: APC1, YNL172W, N1677 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53886 #9: Protein | | Mass: 79355.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: APC5, RMC1, YOR249C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q08683 #10: Protein | Mass: 73197.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: CDC23, YHR166C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P16522 #11: Protein | | Mass: 19377.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SWM1, APC13, YDR260C, YD9320A.11, YD9320A.11c / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12379 #12: Protein | | Mass: 42881.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MND2, YIR025W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40577 #13: Protein | | Mass: 75345.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: APC4, YDR118W / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q04601 #14: Protein | | Mass: 100099.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: APC2, RSI1, YLR127C, L3105, L3108 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12440 #15: Protein | | Mass: 18887.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: APC11, YDL008W, D2900 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q12157, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Protein , 2 types, 2 molecules BS
#6: Protein | Mass: 62903.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CDH1, GI527_G0002420 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A6A5PYD7 |
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#7: Protein | Mass: 169861.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HSL1, GI527_G0003535 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8H4BYV4 |
-Non-polymers , 1 types, 3 molecules
#16: Chemical |
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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: Anaphase promoting complex/cyclosome (APC/C) in complex with Cdh1 and Hsl1 Type: COMPLEX Details: Anaphase promoting complex/cyclosome (APC/C) in complex with Cdh1 and D-box of Hsl1 substrate Entity ID: #1-#15 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 1.1893 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | |||||||||||||||
Buffer solution | pH: 8.3 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1600 nm / C2 aperture diameter: 51 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K |
Image recording | Average exposure time: 2 sec. / Electron dose: 59 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12006 |
Image scans | Width: 1 / Height: 1 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249193 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 190.73 Å2 | ||||||||||||||||||||||||||||||
Refine LS restraints |
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