[English] 日本語
Yorodumi
- EMDB-0899: High resolution structure of FANCA C-terminal domain (CTD) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0899
TitleHigh resolution structure of FANCA C-terminal domain (CTD)
Map data
Sample
  • Complex: FANCA
    • Protein or peptide: Fanconi anemia complementation group A
Keywordsnuclear localization / fanconi anemia core protein / fanconi anemia complementation group a / interstrand crosslink repair / DNA REPAIR
Function / homologyFanconi anaemia group A protein / Fanconi anaemia group A protein, N-terminal domain / Fanconi anaemia group A protein / Fanconi anaemia group A protein N terminus / Fanconi anaemia nuclear complex / interstrand cross-link repair / membrane / FA complementation group A L homeolog
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsJeong E / Lee S
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A2A1A19021035 Korea, Republic Of
National Research Foundation (NRF, Korea)2017M3A9F6029733 Korea, Republic Of
CitationJournal: Nucleic Acids Res / Year: 2020
Title: Structural basis of the fanconi anemia-associated mutations within the FANCA and FANCG complex.
Authors: Eunyoung Jeong / Seong-Gyu Lee / Hyun-Suk Kim / Jihyeon Yang / Jinwoo Shin / Youngran Kim / Jihan Kim / Orlando D Schärer / Youngjin Kim / Jung-Eun Yeo / Ho Min Kim / Yunje Cho /
Abstract: Monoubiquitination of the Fanconi anemia complementation group D2 (FANCD2) protein by the FA core ubiquitin ligase complex is the central event in the FA pathway. FANCA and FANCG play major roles in ...Monoubiquitination of the Fanconi anemia complementation group D2 (FANCD2) protein by the FA core ubiquitin ligase complex is the central event in the FA pathway. FANCA and FANCG play major roles in the nuclear localization of the FA core complex. Mutations of these two genes are the most frequently observed genetic alterations in FA patients, and most point mutations in FANCA are clustered in the C-terminal domain (CTD). To understand the basis of the FA-associated FANCA mutations, we determined the cryo-electron microscopy (EM) structures of Xenopus laevis FANCA alone at 3.35 Å and 3.46 Å resolution and two distinct FANCA-FANCG complexes at 4.59 and 4.84 Å resolution, respectively. The FANCA CTD adopts an arc-shaped solenoid structure that forms a pseudo-symmetric dimer through its outer surface. FA- and cancer-associated point mutations are widely distributed over the CTD. The two different complex structures capture independent interactions of FANCG with either FANCA C-terminal HEAT repeats, or the N-terminal region. We show that mutations that disturb either of these two interactions prevent the nuclear localization of FANCA, thereby leading to an FA pathway defect. The structure provides insights into the function of FANCA CTD, and provides a framework for understanding FA- and cancer-associated mutations.
History
DepositionDec 10, 2019-
Header (metadata) releaseMar 25, 2020-
Map releaseMar 25, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6lhu
  • Surface level: 1.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0899.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 1.02 / Movie #1: 1.02
Minimum - Maximum-3.4176133 - 6.4868164
Average (Standard dev.)-0.00028581926 (±0.11877703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-3.4186.487-0.000

-
Supplemental data

-
Sample components

-
Entire : FANCA

EntireName: FANCA
Components
  • Complex: FANCA
    • Protein or peptide: Fanconi anemia complementation group A

-
Supramolecule #1: FANCA

SupramoleculeName: FANCA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: homo dimer
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 500 kDa/nm

-
Macromolecule #1: Fanconi anemia complementation group A

MacromoleculeName: Fanconi anemia complementation group A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 163.009344 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MWSHPQFEKG SGGSGMSAVS GFTPSGQKRS LAELLDGRVK RLDRKSNNSV LQEAALYLLS CNQDVSQFLS EVEAPPYKKT CNPENPVSI KSRMPSAAFV GSTLKDQASC LKISPGILTA KAAVANIQQI CQACGDSSAV LNPEQREKLC SLLKTLKILL A ENCFCRSL ...String:
MWSHPQFEKG SGGSGMSAVS GFTPSGQKRS LAELLDGRVK RLDRKSNNSV LQEAALYLLS CNQDVSQFLS EVEAPPYKKT CNPENPVSI KSRMPSAAFV GSTLKDQASC LKISPGILTA KAAVANIQQI CQACGDSSAV LNPEQREKLC SLLKTLKILL A ENCFCRSL FCKEIWIHRP PLVFEAVWHL HNEGIVCLDE ILESCKDTIS AVDWLFSEMC SLCLYIDNSS LAGDLAEKMI SD FQALLVE NSFRRSSATE RILEQHKTEE ICLSILDKLL SWLLDAVSVE KSDKSSAEQH WLSAFEVHRY RARVVPESIE QFF IHTLTQ VLTFKPKLKV SDAIQCQANW SFVKTSTLLT DLYRKLFVAL SAEKLIAHIQ LVLDTQEVNW HHVLTCVSCL VICL PEAQQ LIKDLLCRLL THAFESYELE GMITAFLIVR QAALEGPAAF VSYTEWFKCT FGAANSYHGN SKKSLVFLLK FLSDI VPFE APQYLKVHVL HPPFVPTKYR PLLMEYISLA KTRLTDMKVS IEDMGLYEDL SARSNKVQPE SQAHQDVEKA LNIFEN TGK IPASVMEASI FRRPYFTSRF LPALLTPRVL PAAPDALMLL IDSMKRADKI PTNMFNAYIE ACEQEKLRKQ KGRQQMD QS LPDEPLGILQ SALSDLRPLV TDANKYEDVS AQVAVISEKL IAVMGEQKVD DDQVAAKFLK LEDGAQLDIQ EQTVADLL L TCFCQCLIAA SGTNPPDRQG QWPTLYVKML CGHQWAFAAV LRRMLQLLRF QAPFLKDSHI VGLAAFSIHL HECQPSLQF LITGVQNLEH YWENLLNLLC SDSVGVCLKL CTAAISYAFC RFSELHQDIF SGCVPPLFLR KLQYLVPRLI WETRGEVIRD DEEADSPLN WNLYALAGWK EAALSLWNQN RLQGLLREKS FQVTFMDWLL WEMTLKSNND VLCDTDRQEY QRWAVNHYLS E SSVVGGCN GDLERGCITI AEAVLQFSNR HIQHSEWESR NISMLKSHTG LGDILCRLQE LICDIVTSHH QKGRRHFFFA IF YQRLELH KGKKELSNHL SKQGVLEMCC RILLGLPPLF LINTPSEKGI RTLGSEDFWQ FVNKELKNLG PRGYALPYNI TAH FFRGVI SASVQCKDSS EAVNSILSAT YSTCPALLIS AAVGWPQLDP VLRSQWCSLF GVDLPKELRT LREQQASVDS CLSQ GEKLS LSCTPWLSAA FLYSTVQRKK LPCSRMLEIL DGLSSNFSMV LISLLFFSVM DIIYMFLKDG RKHKDLLENC VHIIH CLEQ KGETWVWLFQ MTDERKPELG LHLHRAASDV FLNLMPFAFF WLVPSLQLEQ VVQQQDFLVI ALDMYHKFLQ LFVDGS PLS SLSAKSHHLD SHDVFTCGRQ FLLCCVPKCQ KPNSAILKKM LESWEEHDPE LAAVLTRSFK APDDYDDLFF EPVF

UniProtKB: FA complementation group A L homeolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 150141

+
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