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- PDB-8a5y: S. cerevisiae apo unphosphorylated APC/C. -

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Basic information

Entry
Database: PDB / ID: 8a5y
TitleS. cerevisiae apo unphosphorylated APC/C.
Components(Anaphase-promoting complex subunit ...) x 13
KeywordsCELL 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 / 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 / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of mitotic metaphase/anaphase transition / exit from mitosis / protein K11-linked ubiquitination / positive regulation of protein autoubiquitination / reciprocal meiotic recombination / regulation of mitotic metaphase/anaphase transition / mitotic sister chromatid segregation / ligase activity / ubiquitin ligase inhibitor activity / cullin family protein binding / 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 / cytosol / cytoplasm
Similarity search - Function
Anaphase-promoting complex subunit 15/mnd2 / Anaphase-promoting complex subunit Mnd2 / Anaphase-promoting complex, subunit 9 / Apc15p protein / Anaphase-promoting complex subunit 9 / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex subunit 4 ...Anaphase-promoting complex subunit 15/mnd2 / Anaphase-promoting complex subunit Mnd2 / Anaphase-promoting complex, subunit 9 / Apc15p protein / Anaphase-promoting complex subunit 9 / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit APC10/Doc1 / Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Anaphase-promoting complex, cyclosome, subunit 3 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / TPR repeat / Tetratricopeptide repeat / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Anaphase-promoting complex subunit CDC16 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit CDC23 / Anaphase-promoting complex subunit CDC27 / Anaphase-promoting complex subunit MND2 / Anaphase-promoting complex subunit DOC1 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 9 ...Anaphase-promoting complex subunit CDC16 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit CDC23 / Anaphase-promoting complex subunit CDC27 / Anaphase-promoting complex subunit MND2 / Anaphase-promoting complex subunit DOC1 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 9 / Anaphase-promoting complex subunit 11 / Anaphase-promoting complex subunit SWM1 / Anaphase-promoting complex subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsBarford, D. / Fernandez-Vazquez, E. / Zhang, Z. / Yang, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of the S. cerevisiae APC/C-Cdh1 complex and comparison to apo unphosphorylated and phosphorylated states
Authors: Barford, D. / Fernandez-Vazquez, E. / Zhang, Z. / Yang, J.
History
DepositionJun 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 26, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Anaphase-promoting complex subunit CDC27
J: Anaphase-promoting complex subunit CDC16
K: Anaphase-promoting complex subunit CDC16
G: Anaphase-promoting complex subunit CDC26
W: Anaphase-promoting complex subunit CDC26
H: Anaphase-promoting complex subunit CDC27
E: Anaphase-promoting complex subunit 9
T: Anaphase-promoting complex subunit 2
U: Anaphase-promoting complex subunit 11
C: Anaphase-promoting complex subunit 1
O: Anaphase-promoting complex subunit 5
D: Anaphase-promoting complex subunit CDC23
P: Anaphase-promoting complex subunit CDC23
I: Anaphase-promoting complex subunit SWM1
N: Anaphase-promoting complex subunit MND2
Q: Anaphase-promoting complex subunit 4
A: Anaphase-promoting complex subunit DOC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,130,35820
Polymers1,130,16117
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area82720 Å2
ΔGint-473 kcal/mol
Surface area319840 Å2
MethodPISA

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Components

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Anaphase-promoting complex subunit ... , 13 types, 17 molecules FHJKGWETUCODPINQA

#1: Protein Anaphase-promoting complex subunit CDC27 / / Anaphase-promoting complex subunit 3 / Cell division control protein 27


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 Anaphase-promoting complex subunit CDC16 / / Cell division control protein 16


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 Anaphase-promoting complex subunit CDC26 / / Cell division control protein 26


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 Anaphase-promoting complex subunit 9 /


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 Anaphase-promoting complex subunit 2 /


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
#6: Protein Anaphase-promoting complex subunit 11 /


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)
#7: Protein Anaphase-promoting complex subunit 1 /


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
#8: Protein Anaphase-promoting complex subunit 5 /


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
#9: Protein Anaphase-promoting complex subunit CDC23 / / Cell division control protein 23


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
#10: Protein Anaphase-promoting complex subunit SWM1 / / Anaphase-promoting complex subunit 13 / Spore wall maturation protein 1


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
#11: Protein Anaphase-promoting complex subunit MND2 / / Meiotic nuclear division protein 2


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
#12: Protein Anaphase-promoting complex subunit 4 /


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
#13: Protein Anaphase-promoting complex subunit DOC1 / / Destruction of cyclin B protein 1


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

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Non-polymers , 1 types, 3 molecules

#14: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Anaphase promoting complex/cyclosome (APC/C)COMPLEXApo unphosphorylated anaphase promoting complex/cyclosome (APC/C)#1-#130RECOMBINANT
2unphosphorylated apo APC/C complexCOMPLEX#1-#131RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.13 MDaNO
211.127 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Trichoplusia ni (cabbage looper)7111
32Trichoplusia ni (cabbage looper)7111
Buffer solutionpH: 8.3
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris.HCl1
2250 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 9000 nm / Nominal defocus min: 2600 nm / C2 aperture diameter: 51 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 70 K / Temperature (min): 70 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 59 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4362
Image scansWidth: 1 / Height: 1

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4520refinement
PHENIXdev_4520refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf3CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3initial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 815009
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 372535 / Algorithm: FOURIER SPACE / Num. of class averages: 10 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 274.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004159079
ELECTRON MICROSCOPYf_angle_d0.878579966
ELECTRON MICROSCOPYf_chiral_restr0.05099031
ELECTRON MICROSCOPYf_plane_restr0.004610103
ELECTRON MICROSCOPYf_dihedral_angle_d4.27777776

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