[English] 日本語
Yorodumi
- EMDB-3476: Structure of FANCI-FANCD2 hetero-dimer co-expressed with FANCC-FA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3476
TitleStructure of FANCI-FANCD2 hetero-dimer co-expressed with FANCC-FANCE-FANCF proteins.
Map data3D Reconstruction by negative stain EM of FANCI-FANCD2 co-expressed with FANCC-FANCE-FANCF.
Sample
  • Complex: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly co-expressed with the FANCC-FANCE-FANCF ternary complex.
Methodsingle particle reconstruction / negative staining / Resolution: 18.3 Å
AuthorsSwuec P / Costa A
CitationJournal: Cell Rep / Year: 2017
Title: The FA Core Complex Contains a Homo-dimeric Catalytic Module for the Symmetric Mono-ubiquitination of FANCI-FANCD2.
Authors: Paolo Swuec / Ludovic Renault / Aaron Borg / Fenil Shah / Vincent J Murphy / Sylvie van Twest / Ambrosius P Snijders / Andrew J Deans / Alessandro Costa /
Abstract: Activation of the main DNA interstrand crosslink repair pathway in higher eukaryotes requires mono-ubiquitination of FANCI and FANCD2 by FANCL, the E3 ligase subunit of the Fanconi anemia core ...Activation of the main DNA interstrand crosslink repair pathway in higher eukaryotes requires mono-ubiquitination of FANCI and FANCD2 by FANCL, the E3 ligase subunit of the Fanconi anemia core complex. FANCI and FANCD2 form a stable complex; however, the molecular basis of their ubiquitination is ill defined. FANCD2 mono-ubiquitination by FANCL is stimulated by the presence of the FANCB and FAAP100 core complex components, through an unknown mechanism. How FANCI mono-ubiquitination is achieved remains unclear. Here, we use structural electron microscopy, combined with crosslink-coupled mass spectrometry, to find that FANCB, FANCL, and FAAP100 form a dimer of trimers, containing two FANCL molecules that are ideally poised to target both FANCI and FANCD2 for mono-ubiquitination. The FANCC-FANCE-FANCF subunits bridge between FANCB-FANCL-FAAP100 and the FANCI-FANCD2 substrate. A transient interaction with FANCC-FANCE-FANCF alters the FANCI-FANCD2 configuration, stabilizing the dimerization interface. Our data provide a model to explain how equivalent mono-ubiquitination of FANCI and FANCD2 occurs.
History
DepositionNov 10, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseDec 14, 2016-
UpdateJan 25, 2017-
Current statusJan 25, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.066
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.066
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3476.png

Downloads & links

-
Map

FileDownload / File: emd_3476.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D Reconstruction by negative stain EM of FANCI-FANCD2 co-expressed with FANCC-FANCE-FANCF.
Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy AUTHOR: 0.66 / Movie #1: 0.066
Minimum - Maximum-0.07751421 - 0.1914667
Average (Standard dev.)0.000493103 (±0.012086637)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.0780.1910.000

-
Supplemental data

-
Sample components

-
Entire : Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly...

EntireName: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly co-expressed with the FANCC-FANCE-FANCF ternary complex.
Components
  • Complex: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly co-expressed with the FANCC-FANCE-FANCF ternary complex.

-
Supramolecule #1: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly...

SupramoleculeName: Hetero-dimeric complex of FANCI and FANCD2 proteins recombinantly co-expressed with the FANCC-FANCE-FANCF ternary complex.
type: complex / ID: 1 / Parent: 0
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.005 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
120.0 mMNaClSodium chloridesodium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine
StainingType: NEGATIVE / Material: Uranyl formate
Details: The sample stained with a fresh 2% (wt/vol) uranyl formate solution.
GridModel: 3.05mm diameter, square mesh grids. / Material: COPPER / Mesh: 600 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 4.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Details: Prior to sample incubation, the carbon-coated grid was glow-discharged for 30 seconds at 45 mA.

-
Electron microscopy

MicroscopeJEOL 2100
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: JEOL
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 447 / Average electron dose: 35.0 e/Å2

-
Image processing

Particle selectionNumber selected: 71295
CTF correctionSoftware: (Name: CTFFIND (ver. 3), RELION (ver. 1.4))
Startup modelType of model: INSILICO MODEL
In silico model: For three-dimensional reconstruction of the ID2 complex co-expressed with the CEF complex an initial 3D volume was generated using the e2inimodel.py program in the EMAN2 package. The ...In silico model: For three-dimensional reconstruction of the ID2 complex co-expressed with the CEF complex an initial 3D volume was generated using the e2inimodel.py program in the EMAN2 package. The initial volume was used as reference model for three-dimensional classification and refinement in RELION 1.4.
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 13546

+
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