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- EMDB-2925: Cryo-EM structure of the human APC/C-Cdh1-Hsl1-UbcH10-Ub complex. -

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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 / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of exit from mitosis / free ubiquitin chain polymerization / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase ...negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of exit from mitosis / free ubiquitin chain polymerization / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / positive regulation of synaptic plasticity / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / protein branched polyubiquitination / Phosphorylation of the APC/C / anaphase-promoting complex binding / regulation of exit from mitosis / positive regulation of dendrite morphogenesis / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / exit from mitosis / ubiquitin ligase activator activity / positive regulation of ubiquitin-dependent protein catabolic process / protein K11-linked ubiquitination / regulation of mitotic metaphase/anaphase transition / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / mitotic metaphase chromosome alignment / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like protein ligase binding / Transcriptional Regulation by VENTX / Antigen processing: Ubiquitination & Proteasome degradation / cullin family protein binding / ubiquitin ligase complex / enzyme-substrate adaptor activity / positive regulation of axon extension / protein K48-linked ubiquitination / heterochromatin / intercellular bridge / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / cyclin binding / nuclear periphery / regulation of mitotic cell cycle / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / G protein-coupled receptor binding / brain development / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / spindle / protein polyubiquitination / neuron projection development / ubiquitin-protein transferase activity / positive regulation of protein catabolic process / mitotic spindle / Separation of Sister Chromatids / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / mitotic cell cycle / microtubule cytoskeleton / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein ubiquitination / negative regulation of gene expression / cell division / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / centrosome / nucleolus / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain ...Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / 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 5, N-terminal domain / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / 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 / 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 / : / : / Cullin / Tetratricopeptide repeat / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing 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

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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
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  • 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

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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.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 200 pix.
= 354. Å		1.77 Å/pix.
x 200 pix.
= 354. Å		1.77 Å/pix.
x 200 pix.
= 354. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
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

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Supplemental data

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Sample components

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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

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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

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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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

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Electron microscopy

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

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Image processing

DetailsThe particles were selected using an automatic selection program
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

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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.

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