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- PDB-6lhv: Structure of FANCA and FANCG Complex -

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Basic information

Entry
Database: PDB / ID: 6lhv
TitleStructure of FANCA and FANCG Complex
Components
  • Fanconi anemia complementation group A
  • Fanconi anemia complementation group G
KeywordsDNA REPAIR / nuclear localization / fanconi anemia core protein / fanconi anemia complementation group a / fanconi anemia complementation group g / interstrand crosslink repair
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.59 Å
AuthorsJeong, E. / Lee, S. / Shin, J. / Kim, Y. / 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.
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
Revision 1.2Mar 27, 2024Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)170,2633
Polymers170,2633
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2290 Å2
ΔGint-22 kcal/mol
Surface area104670 Å2

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Components

#1: Protein Fanconi anemia complementation group G


Mass: 34059.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: fancg, FANCG / Production host: Trichoplusia ni (cabbage looper)
#2: Protein Fanconi anemia complementation group A


Mass: 68101.625 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)
Sequence detailsThe authors know the complete sequence as follows. But they are not sure which part of sequential ...The authors know the complete sequence as follows. But they are not sure which part of sequential amino acids corresponds with sample sequence. So the number of residues is meaningless. chain C sequence MDYKDDDDKDYKDDDDKGSGGSGMAGDCLTLWMEENNVIVNQWRDSASYANTFTEKQKLQLLHADLYQLLQKIQGLPATPQSLPLELSVLYNMLIFHIHST SGFQDEHNKHIAETLSRVLRVCSPGVNVQSNEELWHQLVHGGYSSELAASLHRLAGLQGALWLAEEKLQEVHDLFSLLLHPEDSECSTNLRAEEKLLALLK AWRVSNEAEEKVLVVQPAQQLRDVLYTSAAFLQGILAMEASQHPYAINLFGEAAESLCSGRVLAQVYTCLGFCFQKMEKPQTALQYWKQALHLDFQCLAAL YHSSSVYKEMGNVDAELEALNLLYKALLSPEQEAPSTKTCFLIGTEQIVNAPSLTSAVRAPSPWKVKYLIARRCLENKRGEEAVEHYLDLLALLQDESHQD LLPNPEPLIRIPEVFLETAAGLVLEKRYQDAMTVCEEVLGRTDDLIPGSLSVDSTQSKSNVMAEQLNLVLWASAAHLHQGLSHGLLGDQKESVTEYTKCIN LLVKVQFIDTGCASPHCSRGSGDEMEISLIGLCSKEETVLCALKAAAFLGRSRQFLALGKHKESLLNMQLSLQASPAFPGAALTLVGHLIKLGRRTEAGSY LKRYQSERKTLADQWEAMKRNLPLYLDPHINHTFPAEDSLIKELEESAEEMQSEAVV chain B,A sequence MWSHPQFEKGSGGSGMSAVSGFTPSGQKRSLAELLDGRVKRLDRKSNNSVLQEAALYLLSCNQDVSQFLSEVEAPPYKKTCNPENPVSIKSRMPSAAFVGS TLKDQASCLKISPGILTAKAAVANIQQICQACGDSSAVLNPEQREKLCSLLKTLKILLAENCFCRSLFCKEIWIHRPPLVFEAVWHLHNEGIVCLDEILES CKDTISAVDWLFSEMCSLCLYIDNSSLAGDLAEKMISDFQALLVENSFRRSSATERILEQHKTEEICLSILDKLLSWLLDAVSVEKSDKSSAEQHWLSAFE VHRYRARVVPESIEQFFIHTLTQVLTFKPKLKVSDAIQCQANWSFVKTSTLLTDLYRKLFVALSAEKLIAHIQLVLDTQEVNWHHVLTCVSCLVICLPEAQ QLIKDLLCRLLTHAFESYELEGMITAFLIVRQAALEGPAAFVSYTEWFKCTFGAANSYHGNSKKSLVFLLKFLSDIVPFEAPQYLKVHVLHPPFVPTKYRP LLMEYISLAKTRLTDMKVSIEDMGLYEDLSARSNKVQPESQAHQDVEKALNIFENTGKIPASVMEASIFRRPYFTSRFLPALLTPRVLPAAPDALMLLIDS MKRADKIPTNMFNAYIEACEQEKLRKQKGRQQMDQSLPDEPLGILQSALSDLRPLVTDANKYEDVSAQVAVISEKLIAVMGEQKVDDDQVAAKFLKLEDGA QLDIQEQTVADLLLTCFCQCLIAASGTNPPDRQGQWPTLYVKMLCGHQWAFAAVLRRMLQLLRFQAPFLKDSHIVGLAAFSIHLHECQPSLQFLITGVQNL EHYWENLLNLLCSDSVGVCLKLCTAAISYAFCRFSELHQDIFSGCVPPLFLRKLQYLVPRLIWETRGEVIRDDEEADSPLNWNLYALAGWKEAALSLWNQN RLQGLLREKSFQVTFMDWLLWEMTLKSNNDVLCDTDRQEYQRWAVNHYLSESSVVGGCNGDLERGCITIAEAVLQFSNRHIQHSEWESRNISMLKSHTGLG DILCRLQELICDIVTSHHQKGRRHFFFAIFYQRLELHKGKKELSNHLSKQGVLEMCCRILLGLPPLFLINTPSEKGIRTLGSEDFWQFVNKELKNLGPRGY ALPYNITAHFFRGVISASVQCKDSSEAVNSILSATYSTCPALLISAAVGWPQLDPVLRSQWCSLFGVDLPKELRTLREQQASVDSCLSQGEKLSLSCTPWL SAAFLYSTVQRKKLPCSRMLEILDGLSSNFSMVLISLLFFSVMDIIYMFLKDGRKHKDLLENCVHIIHCLEQKGETWVWLFQMTDERKPELGLHLHRAASD VFLNLMPFAFFWLVPSLQLEQVVQQQDFLVIALDMYHKFLQLFVDGSPLSSLSAKSHHLDSHDVFTCGRQFLLCCVPKCQKPNSAILKKMLESWEEHDPEL AAVLTRSFKAPDDYDDLFFEPVF

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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: all / 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 recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1130FEI FALCON III (4k x 4k)
2130FEI FALCON III (4k x 4k)
3130FEI FALCON III (4k x 4k)
4130FEI FALCON III (4k x 4k)
5130FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89678 / Symmetry type: POINT

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