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- EMDB-2353: Anaphase Promoting Complex with an Emi1 deletion mutant bound -

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Basic information

Entry
Database: EMDB / ID: EMD-2353
TitleAnaphase Promoting Complex with an Emi1 deletion mutant bound
Map dataAnaphase Promoting Complex with Emi1 deletion mutant
Sample
  • Sample: APC/C - Emi1 mutant complex
  • Protein or peptide: APC/C
  • Protein or peptide: Emi1
Keywordscell cycle regulation
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsFrye JJ / Brown NG / Petzold G / Watson ER / Grace CRR / Nourse A / Jarvis M / Kriwacki RW / Peters JM / Stark H / Schulman BA
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Electron microscopy structure of human APC/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown.
Authors: Jeremiah J Frye / Nicholas G Brown / Georg Petzold / Edmond R Watson / Christy R R Grace / Amanda Nourse / Marc A Jarvis / Richard W Kriwacki / Jan-Michael Peters / Holger Stark / Brenda A Schulman /
Abstract: The anaphase-promoting complex/cyclosome (APC/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle ...The anaphase-promoting complex/cyclosome (APC/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle regulatory proteins. Inhibition of human APC/C(CDH1) during interphase by early mitotic inhibitor 1 (EMI1) is essential for accurate coordination of DNA synthesis and mitosis. Here, we report a hybrid structural approach involving NMR, electron microscopy and enzymology, which reveal that EMI1's 143-residue C-terminal domain inhibits multiple APC/C(CDH1) functions. The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation. The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down various functions of a 'molecular machine' nearly 100 times its size.
History
DepositionApr 6, 2013-
Header (metadata) releaseApr 17, 2013-
Map releaseAug 7, 2013-
UpdateAug 7, 2013-
Current statusAug 7, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2353_305...

Downloads & links

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Map

FileDownload / File: emd_2353.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnaphase Promoting Complex with Emi1 deletion mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5 Å/pix.
x 80 pix.
= 400. Å		5 Å/pix.
x 80 pix.
= 400. Å		5 Å/pix.
x 80 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.0 / Movie #1: 11
Minimum - Maximum-86.776855470000001 - 138.02041625999999
Average (Standard dev.)0.00000012 (±9.999990459999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z555
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-86.777138.0200.000

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Supplemental data

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Sample components

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Entire : APC/C - Emi1 mutant complex

EntireName: APC/C - Emi1 mutant complex
Components
  • Sample: APC/C - Emi1 mutant complex
  • Protein or peptide: APC/C
  • Protein or peptide: Emi1

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Supramolecule #1000: APC/C - Emi1 mutant complex

SupramoleculeName: APC/C - Emi1 mutant complex / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 1.6 MDa

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Macromolecule #1: APC/C

MacromoleculeName: APC/C / type: protein_or_peptide / ID: 1 / Name.synonym: Anaphase Promoting Complex / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Macromolecule #2: Emi1

MacromoleculeName: Emi1 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: 20mM Tris-HCL, 150 mM NaCl
StainingType: NEGATIVE / Details: Uranyl Formate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateFeb 10, 2013
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 118800 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Software - Name: Imagic / Number images used: 12935

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