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- EMDB-2775: Mechanism of polyubiquitination by human Anaphase Promoting Compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-2775
TitleMechanism of polyubiquitination by human Anaphase Promoting Complex: RING repurposing for ubiquitin chain assembly
Map dataAPC/C 3D structure with Ube2S bound
Sample
  • Sample: Anaphase Promoting Complex with bound Ube2S
  • Protein or peptide: Anapahse Promoting Complex
  • Protein or peptide: Ube2S
KeywordsUbiquitination / APC/C / RING / Ube2S
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsBrown 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
CitationJournal: 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
DepositionSep 2, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseOct 22, 2014-
UpdateNov 19, 2014-
Current statusNov 19, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2775.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAPC/C 3D structure with Ube2S bound
Voxel sizeX=Y=Z: 4 Å
Density
Contour LevelBy AUTHOR: 28.0 / Movie #1: 28
Minimum - Maximum-52.336269379999997 - 125.329544069999997
Average (Standard dev.)1.30136847 (±8.412844659999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z444
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-52.336125.3301.301

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Supplemental data

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Sample components

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Entire : Anaphase Promoting Complex with bound Ube2S

EntireName: Anaphase Promoting Complex with bound Ube2S
Components
  • Sample: Anaphase Promoting Complex with bound Ube2S
  • Protein or peptide: Anapahse Promoting Complex
  • Protein or peptide: Ube2S

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Supramolecule #1000: Anaphase Promoting Complex with bound Ube2S

SupramoleculeName: Anaphase Promoting Complex with bound Ube2S / type: sample / ID: 1000 / Number unique components: 2
Molecular weightExperimental: 1.5 MDa / Theoretical: 1.5 MDa

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Macromolecule #1: Anapahse Promoting Complex

MacromoleculeName: Anapahse Promoting Complex / type: protein_or_peptide / ID: 1 / Name.synonym: APC/C / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 1.5 MDa / Theoretical: 1.5 MDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Hela

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Macromolecule #2: Ube2S

MacromoleculeName: Ube2S / type: protein_or_peptide / ID: 2 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant 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

BufferpH: 8 / Details: 20 mM HEPES pH 8.0, 200 mM NaCl
GridDetails: 200 mesh grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 74000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Cs: mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 80 K
Cs0
DateMar 5, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied 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

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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