[English] 日本語
Yorodumi
- EMDB-2929: Mechanism of Ubiquitin Ligation to a Substrate by human Anaphase-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2929
TitleMechanism of Ubiquitin Ligation to a Substrate by human Anaphase-Promoting Complex
Map dataanaphase promoting complexAnaphase-promoting complex
Sample
  • Sample: Cdh1 and UbcH10 bound to Anaphase Promoting Complex
  • Protein or peptide: Anaphase Promoting ComplexAnaphase-promoting complex
KeywordsAnaphase Promoting Complex / ubiquitin ligation
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsBrown N / VanderLinden R / Watson E / Qiao R / Grace CR / Yamaguchi M / Weissmann F / Frye J / Dube P / Cho SE ...Brown N / VanderLinden R / Watson E / Qiao R / Grace CR / Yamaguchi M / Weissmann F / Frye J / Dube P / Cho SE / Actis M / Rodrigues P / Fujii N / Peters JM / Schulman BA / Stark H
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: RING E3 mechanism for ubiquitin ligation to a disordered substrate visualized for human anaphase-promoting complex.
Authors: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Renping Qiao / Christy R R Grace / Masaya Yamaguchi / Florian Weissmann / Jeremiah J Frye / Prakash Dube / Shein Ei Cho / Marcelo L ...Authors: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Renping Qiao / Christy R R Grace / Masaya Yamaguchi / Florian Weissmann / Jeremiah J Frye / Prakash Dube / Shein Ei Cho / Marcelo L Actis / Patrick Rodrigues / Naoaki Fujii / Jan-Michael Peters / Holger Stark / Brenda A Schulman /
Abstract: For many E3 ligases, a mobile RING (Really Interesting New Gene) domain stimulates ubiquitin (Ub) transfer from a thioester-linked E2∼Ub intermediate to a lysine on a remotely bound disordered ...For many E3 ligases, a mobile RING (Really Interesting New Gene) domain stimulates ubiquitin (Ub) transfer from a thioester-linked E2∼Ub intermediate to a lysine on a remotely bound disordered substrate. One such E3 is the gigantic, multisubunit 1.2-MDa anaphase-promoting complex/cyclosome (APC), which controls cell division by ubiquitinating cell cycle regulators to drive their timely degradation. Intrinsically disordered substrates are typically recruited via their KEN-box, D-box, and/or other motifs binding to APC and a coactivator such as CDH1. On the opposite side of the APC, the dynamic catalytic core contains the cullin-like subunit APC2 and its RING partner APC11, which collaborates with the E2 UBCH10 (UBE2C) to ubiquitinate substrates. However, how dynamic RING-E2∼Ub catalytic modules such as APC11-UBCH10∼Ub collide with distally tethered disordered substrates remains poorly understood. We report structural mechanisms of UBCH10 recruitment to APC(CDH1) and substrate ubiquitination. Unexpectedly, in addition to binding APC11's RING, UBCH10 is corecruited via interactions with APC2, which we visualized in a trapped complex representing an APC(CDH1)-UBCH10∼Ub-substrate intermediate by cryo-electron microscopy, and in isolation by X-ray crystallography. To our knowledge, this is the first structural view of APC, or any cullin-RING E3, with E2 and substrate juxtaposed, and it reveals how tripartite cullin-RING-E2 interactions establish APC's specificity for UBCH10 and harness a flexible catalytic module to drive ubiquitination of lysines within an accessible zone. We propose that multisite interactions reduce the degrees of freedom available to dynamic RING E3-E2∼Ub catalytic modules, condense the search radius for target lysines, increase the chance of active-site collision with conformationally fluctuating substrates, and enable regulation.
History
DepositionMar 10, 2015-
Header (metadata) releaseApr 15, 2015-
Map releaseApr 15, 2015-
UpdateMay 13, 2015-
Current statusMay 13, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2929.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationanaphase promoting complex
Voxel sizeX=Y=Z: 1.57 Å
Density
Contour LevelBy AUTHOR: 50.0 / Movie #1: 50
Minimum - Maximum-77.057800290000003 - 177.376434329999995
Average (Standard dev.)0.00011701 (±10.151549340000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 401.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.571.571.57
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z401.920401.920401.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-77.058177.3760.000

-
Supplemental data

-
Sample components

-
Entire : Cdh1 and UbcH10 bound to Anaphase Promoting Complex

EntireName: Cdh1 and UbcH10 bound to Anaphase Promoting Complex
Components
  • Sample: Cdh1 and UbcH10 bound to Anaphase Promoting Complex
  • Protein or peptide: Anaphase Promoting ComplexAnaphase-promoting complex

-
Supramolecule #1000: Cdh1 and UbcH10 bound to Anaphase Promoting Complex

SupramoleculeName: Cdh1 and UbcH10 bound to Anaphase Promoting Complex / type: sample / ID: 1000 / Number unique components: 3
Molecular weightExperimental: 1.5 MDa

-
Macromolecule #1: Anaphase Promoting Complex

MacromoleculeName: Anaphase Promoting Complex / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 8 / Details: 50 mM Hepes, 150 mM NaCl, 2 mM MgCl2
GridDetails: 200 mesh copper grids, quantifoil with thin carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 94000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.0001 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateFeb 18, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 2097 / Average electron dose: 30 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Number images used: 47791

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more