[English] 日本語
Yorodumi
- EMDB-2925: Cryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2925
TitleCryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex.
Map dataCryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex.
Sample
  • Sample: Recombinant human APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex
  • Protein or peptide: x 18 types
KeywordsUbiquitination / 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 / : / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / regulation of mitotic cell cycle spindle assembly checkpoint / free ubiquitin chain polymerization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of synapse maturation ...negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / : / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of exit from mitosis / regulation of mitotic cell cycle spindle assembly checkpoint / free ubiquitin chain polymerization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / 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 / anaphase-promoting complex-dependent catabolic process / regulation of meiotic cell cycle / positive regulation of mitotic metaphase/anaphase transition / metaphase/anaphase transition of mitotic cell cycle / (E3-independent) E2 ubiquitin-conjugating enzyme / regulation of exit from mitosis / positive regulation of synaptic plasticity / Antigen processing: Ubiquitination & Proteasome degradation / Phosphorylation of the APC/C / anaphase-promoting complex binding / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / exit from mitosis / 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 / E2 ubiquitin-conjugating enzyme / mitotic metaphase chromosome alignment / ubiquitin conjugating enzyme activity / ubiquitin-like protein ligase binding / regulation of mitotic cell cycle / cullin family protein binding / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / positive regulation of axon extension / heterochromatin / ubiquitin ligase complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / cyclin binding / 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 / brain development / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / spindle / mitotic spindle / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / Separation of Sister Chromatids / ubiquitin protein ligase activity / microtubule cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / ubiquitin-dependent protein catabolic process / Senescence-Associated Secretory Phenotype (SASP) / protein phosphatase binding / cell differentiation / molecular adaptor activity / 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 / cytosol / cytoplasm
Similarity search - Function
Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : ...Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : / Anaphase-promoting complex subunit 1 WD40 beta-propeller domain / Anaphase-promoting complex sub unit 1 C-terminal domain / Anaphase-promoting complex subunit 1 middle domain / APC1 beta sandwich domain / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Cdc23 / Apc13 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / 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 / 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 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-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 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / APC/C activator protein CDH1 / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 ...Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / APC/C activator protein CDH1 / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 2 / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsChang L / Zhang Z / Yang J / McLaughlin SH / Barford D
CitationJournal: 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
DepositionMar 9, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseJun 17, 2015-
UpdateNov 18, 2015-
Current statusNov 18, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5a31
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2925.jpg

Downloads & links

-
Map

FileDownload / File: emd_2925.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex.
Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy EMDB: 0.07 / Movie #1: 0.09
Minimum - Maximum-0.13345481 - 0.39743313
Average (Standard dev.)0.0046843 (±0.02312339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 354.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z354.000354.000354.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1330.3970.005

-
Supplemental data

-
Sample components

+
Entire : Recombinant human APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex

EntireName: Recombinant human APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex
Components
  • Sample: Recombinant human APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex
  • Protein or peptide: Apc1
  • Protein or peptide: Apc2
  • Protein or peptide: Apc3
  • Protein or peptide: Apc4
  • Protein or peptide: Apc5
  • Protein or peptide: Apc6
  • Protein or peptide: Apc7
  • Protein or peptide: Apc8
  • Protein or peptide: Apc10
  • Protein or peptide: Apc11
  • Protein or peptide: Apc12
  • Protein or peptide: Apc13
  • Protein or peptide: Apc15
  • Protein or peptide: Apc16
  • Protein or peptide: Cdh1
  • Protein or peptide: Hsl1
  • Protein or peptide: E2-ubiquitin conjugate
  • Protein or peptide: UbcH10-ubiquitin

+
Supramolecule #1000: Recombinant human APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex

SupramoleculeName: Recombinant human APC/C-Cdh1-Hsl1-UbcH10LR-Ub complex / type: sample / ID: 1000 / Number unique components: 18
Molecular weightExperimental: 1.2 MDa / Theoretical: 1.2 MDa

+
Macromolecule #1: Apc1

MacromoleculeName: Apc1 / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #2: Apc2

MacromoleculeName: Apc2 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #3: Apc3

MacromoleculeName: Apc3 / type: protein_or_peptide / ID: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #4: Apc4

MacromoleculeName: Apc4 / type: protein_or_peptide / ID: 4 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #5: Apc5

MacromoleculeName: Apc5 / type: protein_or_peptide / ID: 5 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #6: Apc6

MacromoleculeName: Apc6 / type: protein_or_peptide / ID: 6 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #7: Apc7

MacromoleculeName: Apc7 / type: protein_or_peptide / ID: 7 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #8: Apc8

MacromoleculeName: Apc8 / type: protein_or_peptide / ID: 8 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #9: Apc10

MacromoleculeName: Apc10 / type: protein_or_peptide / ID: 9 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #10: Apc11

MacromoleculeName: Apc11 / type: protein_or_peptide / ID: 10 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #11: Apc12

MacromoleculeName: Apc12 / type: protein_or_peptide / ID: 11 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #12: Apc13

MacromoleculeName: Apc13 / type: protein_or_peptide / ID: 12 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #13: Apc15

MacromoleculeName: Apc15 / type: protein_or_peptide / ID: 13 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #14: Apc16

MacromoleculeName: Apc16 / type: protein_or_peptide / ID: 14 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #15: Cdh1

MacromoleculeName: Cdh1 / type: protein_or_peptide / ID: 15 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #16: Hsl1

MacromoleculeName: Hsl1 / type: protein_or_peptide / ID: 16 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #17: E2-ubiquitin conjugate

MacromoleculeName: E2-ubiquitin conjugate / type: protein_or_peptide / ID: 17 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

+
Macromolecule #18: UbcH10-ubiquitin

MacromoleculeName: UbcH10-ubiquitin / type: protein_or_peptide / ID: 18 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 8 / Details: 20 mM HEPES, 150 mM NaCl, 1 mM DTT
GridDetails: R2/2 Quantifoil grid with thin carbon support.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 5 seconds before plunging

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: OTHER
DateJul 12, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 16 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 19939
DetailsThe particles were selected using an automatic selection program

-
Atomic model buiding 1

Initial modelPDB ID:

1i7k


Chain - Chain ID: A
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5a31:
Structure of the human APC-Cdh1-Hsl1-UbcH10 complex.

+
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