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- EMDB-1591: Structure of the anaphase promoting complex interacting with a mi... -

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Basic information

Entry
Database: EMDB / ID: EMD-1591
TitleStructure of the anaphase promoting complex interacting with a mitotic checkpoint complex
Map data3D map of the anaphase promoting complex bound to the mitotic checkpoint complex
Sample
  • Sample: Anaphase promoting complex
  • Protein or peptide: APC
KeywordsAnaphase-promoting complex / Spindle checkpoint / Electron cryomicroscopy / Mitotic checkpoint complex / Cdc20
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsHerzog F / Primorac I / Dube P / Lenart P / Sander B / Mechtler K / Stark H / Peters JM
CitationJournal: Science / Year: 2009
Title: Structure of the anaphase-promoting complex/cyclosome interacting with a mitotic checkpoint complex.
Authors: Franz Herzog / Ivana Primorac / Prakash Dube / Peter Lenart / Björn Sander / Karl Mechtler / Holger Stark / Jan-Michael Peters /
Abstract: Once all chromosomes are connected to the mitotic spindle (bioriented), anaphase is initiated by the protein ubiquitylation activity of the anaphase-promoting complex/cyclosome (APC/C) and its ...Once all chromosomes are connected to the mitotic spindle (bioriented), anaphase is initiated by the protein ubiquitylation activity of the anaphase-promoting complex/cyclosome (APC/C) and its coactivator Cdc20 (APC/C(Cdc20)). Before chromosome biorientation, anaphase is delayed by a mitotic checkpoint complex (MCC) that inhibits APC/C(Cdc20). We used single-particle electron microscopy to obtain three-dimensional models of human APC/C in various functional states: bound to MCC, to Cdc20, or to neither (apo-APC/C). These experiments revealed that MCC associates with the Cdc20 binding site on APC/C, locks the otherwise flexible APC/C in a "closed" state, and prevents binding and ubiquitylation of a wide range of different APC/C substrates. These observations clarify the structural basis for the inhibition of APC/C by spindle checkpoint proteins.
History
DepositionJan 22, 2009-
Header (metadata) releaseFeb 25, 2009-
Map releaseJun 11, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB_1591.gif

Downloads & links

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Map

FileDownload / File: emd_1591.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of the anaphase promoting complex bound to the mitotic checkpoint complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.8 Å/pix.
x 100 pix.
= 380. Å		3.8 Å/pix.
x 100 pix.
= 380. Å		3.8 Å/pix.
x 100 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.419 / Movie #1: 0.12
Minimum - Maximum-0.45102 - 0.883923
Average (Standard dev.)-0.000125138 (±0.0782031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 380 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.83.83.8
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z380.000380.000380.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-165-165-40
NX/NY/NZ33033081
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.4510.884-0.000

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Supplemental data

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Sample components

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Entire : Anaphase promoting complex

EntireName: Anaphase promoting complex
Components
  • Sample: Anaphase promoting complex
  • Protein or peptide: APC

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Supramolecule #1000: Anaphase promoting complex

SupramoleculeName: Anaphase promoting complex / type: sample / ID: 1000 / Number unique components: 15
Molecular weightTheoretical: 1.7 MDa

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Macromolecule #1: APC

MacromoleculeName: APC / type: protein_or_peptide / ID: 1 / Name.synonym: APC / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa

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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

VitrificationCryogen name: NITROGEN / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k)
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsGraFix treated
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å

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