[English] 日本語
Yorodumi
- PDB-8a3t: S. cerevisiae APC/C-Cdh1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a3t
TitleS. cerevisiae APC/C-Cdh1 complex
Components
  • (Anaphase-promoting complex subunit ...) x 13
  • CDH1 isoform 1
  • HSL1 isoform 1
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) / 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 / 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) / ubiquitin-protein transferase activator activity / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex binding / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / exit from mitosis / positive regulation of protein autoubiquitination / protein K11-linked ubiquitination / reciprocal meiotic recombination / regulation of mitotic metaphase/anaphase transition / ligase activity / cullin family protein binding / mitotic sister chromatid segregation / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase inhibitor activity / enzyme regulator activity / negative regulation of DNA-templated DNA replication initiation / cyclin binding / nuclear periphery / regulation of mitotic cell cycle / kinetochore / spindle pole / ubiquitin protein ligase activity / chromatin organization / ubiquitin-dependent protein catabolic process / molecular adaptor activity / protein phosphorylation / protein kinase activity / protein ubiquitination / cell division / ubiquitin protein ligase binding / mitochondrion / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / The WD repeat Cdc20/Fizzy family / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein ...Anaphase-promoting complex subunit 15/mnd2 / Anaphase-promoting complex subunit Mnd2 / Anaphase-promoting complex, subunit 9 / Apc15p protein / Anaphase-promoting complex subunit 9 / The WD repeat Cdc20/Fizzy family / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Tetratricopeptide repeat 2 / 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 / Tetratricopeptide repeat / 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 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Anaphase-promoting complex, cyclosome, subunit 3 / TPR repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / : / Tetratricopeptide repeat / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Galactose-binding domain-like / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats profile. / Jelly Rolls / WD40 repeats / WD40 repeat / Protein kinase domain / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CDH1 isoform 1 / HSL1 isoform 1 / 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 ...CDH1 isoform 1 / HSL1 isoform 1 / 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: 3.5 Å
AuthorsBarford, D. / Vazquez-Fernandez, 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
Authors: Barford, D. / Vazquez-Fernandez, E. / Zhang, Z. / Yang, J.
History
DepositionJun 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
A: Anaphase-promoting complex subunit DOC1
B: CDH1 isoform 1
S: HSL1 isoform 1
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
T: Anaphase-promoting complex subunit 2
U: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,363,12322
Polymers1,362,92619
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area97260 Å2
ΔGint-553 kcal/mol
Surface area325590 Å2
MethodPISA

-
Components

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

#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 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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)

-
Protein , 2 types, 2 molecules BS

#6: Protein CDH1 isoform 1


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
#7: Protein HSL1 isoform 1


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 ChemComp-ZN / ZINC ION


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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 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
Molecular weightValue: 1.1893 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8.3
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisTris.HCl1
2250 mMsodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 298 K

-
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 FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1600 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 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12006
Image scansWidth: 1 / Height: 1

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4520refinement
PHENIXdev_4520refinement
EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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 buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 190.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004362633
ELECTRON MICROSCOPYf_angle_d0.753684786
ELECTRON MICROSCOPYf_chiral_restr0.04279584
ELECTRON MICROSCOPYf_plane_restr0.004810715
ELECTRON MICROSCOPYf_dihedral_angle_d4.25858256

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more