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- EMDB-0899: High resolution structure of FANCA C-terminal domain (CTD) -

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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

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Structure visualization

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

emd_0899.png

Downloads & links

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Map

FileDownload / File: emd_0899.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
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

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Supplemental data

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Sample components

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Entire : FANCA

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

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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

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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

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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

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

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Electron microscopy

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

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Image processing

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

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