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- PDB-6lhu: High resolution structure of FANCA C-terminal domain (CTD) -

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Basic information

Entry
Database: PDB / ID: 6lhu
TitleHigh resolution structure of FANCA C-terminal domain (CTD)
ComponentsFanconi anemia complementation group A
KeywordsDNA REPAIR / nuclear localization / fanconi anemia core protein / fanconi anemia complementation group a / interstrand crosslink repair
Function / homologyFanconi anaemia group A protein / Fanconi anaemia group A protein, N-terminal domain / Fanconi anaemia nuclear complex / interstrand cross-link repair / integral component of membrane / Fanconi anemia complementation group A
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsJeong, E. / Lee, S. / Shin, J. / Kim, Y. / Kim, J. / Scharer, O. / Kim, Y. / Kim, H. / Cho, Y.
Funding support Korea, Republic Of, 2items
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionDec 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
B: Fanconi anemia complementation group A
A: Fanconi anemia complementation group A


Theoretical massNumber of molelcules
Total (without water)326,0192
Polymers326,0192
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5610 Å2
ΔGint-16 kcal/mol
Surface area69660 Å2

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Components

#1: Protein Fanconi anemia complementation group A


Mass: 163009.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: fanca, FANCA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4VT51

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FANCA / Type: COMPLEX / Details: homo dimer / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 500 kDa/nm / Experimental value: YES
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150141 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00424503
ELECTRON MICROSCOPYf_angle_d0.58544274
ELECTRON MICROSCOPYf_dihedral_angle_d8.6079879
ELECTRON MICROSCOPYf_chiral_restr0.0391907
ELECTRON MICROSCOPYf_plane_restr0.0033624

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