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Yorodumi- EMDB-2775: Mechanism of polyubiquitination by human Anaphase Promoting Compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2775 | |||||||||
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Title | Mechanism of polyubiquitination by human Anaphase Promoting Complex: RING repurposing for ubiquitin chain assembly | |||||||||
Map data | APC/C 3D structure with Ube2S bound | |||||||||
Sample |
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Keywords | Ubiquitination / APC/C / RING / Ube2S | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||
Authors | Brown NG / Watson ER / Weissmann F / Jarvis MA / Vanderlinden R / Grace CRR / Frye JJ / Qiao R / Dube P / Petzold G ...Brown NG / Watson ER / Weissmann F / Jarvis MA / Vanderlinden R / Grace CRR / Frye JJ / Qiao R / Dube P / Petzold G / Cho SE / Alsharif O / Bao J / Davidson IF / Zheng J / Nourse A / Kurinov I / Peters JM / Stark H / Schulman BA | |||||||||
Citation | Journal: Mol Cell / Year: 2014 Title: Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly. Authors: Nicholas G Brown / Edmond R Watson / Florian Weissmann / Marc A Jarvis / Ryan VanderLinden / Christy R R Grace / Jeremiah J Frye / Renping Qiao / Prakash Dube / Georg Petzold / Shein Ei Cho ...Authors: Nicholas G Brown / Edmond R Watson / Florian Weissmann / Marc A Jarvis / Ryan VanderLinden / Christy R R Grace / Jeremiah J Frye / Renping Qiao / Prakash Dube / Georg Petzold / Shein Ei Cho / Omar Alsharif / Ju Bao / Iain F Davidson / Jie J Zheng / Amanda Nourse / Igor Kurinov / Jan-Michael Peters / Holger Stark / Brenda A Schulman / Abstract: Polyubiquitination by E2 and E3 enzymes is a predominant mechanism regulating protein function. Some RING E3s, including anaphase-promoting complex/cyclosome (APC), catalyze polyubiquitination by ...Polyubiquitination by E2 and E3 enzymes is a predominant mechanism regulating protein function. Some RING E3s, including anaphase-promoting complex/cyclosome (APC), catalyze polyubiquitination by sequential reactions with two different E2s. An initiating E2 ligates ubiquitin to an E3-bound substrate. Another E2 grows a polyubiquitin chain on the ubiquitin-primed substrate through poorly defined mechanisms. Here we show that human APC's RING domain is repurposed for dual functions in polyubiquitination. The canonical RING surface activates an initiating E2-ubiquitin intermediate for substrate modification. However, APC engages and activates its specialized ubiquitin chain-elongating E2 UBE2S in ways that differ from current paradigms. During chain assembly, a distinct APC11 RING surface helps deliver a substrate-linked ubiquitin to accept another ubiquitin from UBE2S. Our data define mechanisms of APC/UBE2S-mediated polyubiquitination, reveal diverse functions of RING E3s and E2s, and provide a framework for understanding distinctive RING E3 features specifying ubiquitin chain elongation. | |||||||||
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_2775.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-2775-v30.xml emd-2775.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_2775.png | 148.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2775 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2775 | HTTPS FTP |
-Validation report
Summary document | emd_2775_validation.pdf.gz | 201.9 KB | Display | EMDB validaton report |
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Full document | emd_2775_full_validation.pdf.gz | 201 KB | Display | |
Data in XML | emd_2775_validation.xml.gz | 5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2775 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2775 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2775.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | APC/C 3D structure with Ube2S bound | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4 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 : Anaphase Promoting Complex with bound Ube2S
Entire | Name: Anaphase Promoting Complex with bound Ube2S |
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Components |
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-Supramolecule #1000: Anaphase Promoting Complex with bound Ube2S
Supramolecule | Name: Anaphase Promoting Complex with bound Ube2S / type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Experimental: 1.5 MDa / Theoretical: 1.5 MDa |
-Macromolecule #1: Anapahse Promoting Complex
Macromolecule | Name: Anapahse Promoting Complex / type: protein_or_peptide / ID: 1 / Name.synonym: APC/C / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Experimental: 1.5 MDa / Theoretical: 1.5 MDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: Hela |
-Macromolecule #2: Ube2S
Macromolecule | Name: Ube2S / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: Hela |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Details: 20 mM HEPES pH 8.0, 200 mM NaCl |
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Grid | Details: 200 mesh grid with thin carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Cs | 0 |
Temperature | Min: 80 K |
Date | Mar 5, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 74000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Cs: mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: OTHER / Software - Name: in, house, software, Relion / Number images used: 20468 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |