+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2354 | |||||||||
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Title | Anaphase Promoting Complex with full length Emi1 bound | |||||||||
Map data | Anaphase Promoting Complex - Emi1 (full length) | |||||||||
Sample |
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Keywords | cell cycle regulation | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Frye JJ / Brown NG / Petzold G / Watson ER / Grace CRR / Nourse A / Jarvis M / Kriwacki RW / Peters JM / Stark H / Schulman BA | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2354.map.gz | 1.1 MB | EMDB map data format | |
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Header (meta data) | emd-2354-v30.xml emd-2354.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | EMD-2354_full_length_view.jpg | 36.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2354 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2354 | HTTPS FTP |
-Validation report
Summary document | emd_2354_validation.pdf.gz | 198.2 KB | Display | EMDB validaton report |
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Full document | emd_2354_full_validation.pdf.gz | 197.4 KB | Display | |
Data in XML | emd_2354_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2354 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2354 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2354.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Anaphase Promoting Complex - Emi1 (full length) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : APC/C - Emi1 complex
Entire | Name: APC/C - Emi1 complex |
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Components |
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-Supramolecule #1000: APC/C - Emi1 complex
Supramolecule | Name: APC/C - Emi1 complex / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Theoretical: 1.6 MDa |
-Macromolecule #1: APC/C
Macromolecule | Name: APC/C / type: protein_or_peptide / ID: 1 / Name.synonym: Anaphase Promoting Complex / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
-Macromolecule #2: Emi1
Macromolecule | Name: Emi1 / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Details: 20mM Tris-HCL, 150 mM NaCl |
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Staining | Type: NEGATIVE / Details: Uranyl Formate |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Date | Jun 13, 2012 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 118800 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Software - Name: Imagic / Number images used: 18911 |