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- EMDB-50355: dsDNA-FANCD2-FANCI complex -

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Basic information

Entry
Database: EMDB / ID: EMD-50355
TitledsDNA-FANCD2-FANCI complex
Map dataConsensus map dsDNA-D2-I complex
Sample
  • Complex: dsDNA-FANCD2-FANCI complex
    • Protein or peptide: Fanconi anemia protein FANCD2
    • Protein or peptide: Fanconi anemia complementation group I
    • DNA: DNA (32-MER)
    • DNA: DNA (33-MER)
KeywordsdsDNA-FANCD2-FANCI / Fanconi Anemia / D2-I complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


Fanconi Anemia Pathway in DNA repair / DNA repair / nucleoplasm
Similarity search - Function
Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 ...Fanconi anemia group I protein / FANCI solenoid 1 cap / FANCI solenoid 1 domain / FANCI helical domain 1 / FANCI helical domain 2 / FANCI solenoid 3 domain / FANCI solenoid 4 domain / FANCI solenoid 2 domain / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 4 / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FANCD2 / Fanconi anaemia protein FancD2 nuclease
Similarity search - Domain/homology
Fanconi anemia complementation group I / Fanconi anemia protein FANCD2
Similarity search - Component
Biological speciesGallus gallus (chicken) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsAlcon P / Passmore LA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105192715 United Kingdom
CitationJournal: Nature / Year: 2024
Title: FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions.
Authors: Pablo Alcón / Artur P Kaczmarczyk / Korak Kumar Ray / Themistoklis Liolios / Guillaume Guilbaud / Tamara Sijacki / Yichao Shen / Stephen H McLaughlin / Julian E Sale / Puck Knipscheer / ...Authors: Pablo Alcón / Artur P Kaczmarczyk / Korak Kumar Ray / Themistoklis Liolios / Guillaume Guilbaud / Tamara Sijacki / Yichao Shen / Stephen H McLaughlin / Julian E Sale / Puck Knipscheer / David S Rueda / Lori A Passmore /
Abstract: DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2-FANCI (D2-I) protein complex is central to this process as it initiates repair by coordinating DNA ...DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2-FANCI (D2-I) protein complex is central to this process as it initiates repair by coordinating DNA incisions around the lesion. However, D2-I is also known to have a more general role in DNA repair and in protecting stalled replication forks from unscheduled degradation. At present, it is unclear how DNA crosslinks are recognized and how D2-I functions in replication fork protection. Here, using single-molecule imaging, we show that D2-I is a sliding clamp that binds to and diffuses on double-stranded DNA. Notably, sliding D2-I stalls on encountering single-stranded-double-stranded (ss-ds) DNA junctions, structures that are generated when replication forks stall at DNA lesions. Using cryogenic electron microscopy, we determined structures of D2-I on DNA that show that stalled D2-I makes specific interactions with the ss-dsDNA junction that are distinct from those made by sliding D2-I. Thus, D2-I surveys dsDNA and, when it reaches an ssDNA gap, it specifically clamps onto ss-dsDNA junctions. Because ss-dsDNA junctions are found at stalled replication forks, D2-I can identify sites of DNA damage. Therefore, our data provide a unified molecular mechanism that reconciles the roles of D2-I in the recognition and protection of stalled replication forks in several DNA repair pathways.
History
DepositionMay 23, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50355.png

Downloads & links

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Map

FileDownload / File: emd_50355.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map dsDNA-D2-I complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 450 pix.
= 371.25 Å		0.83 Å/pix.
x 450 pix.
= 371.25 Å		0.83 Å/pix.
x 450 pix.
= 371.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.0070471596 - 0.017280128
Average (Standard dev.)0.000019637097 (±0.00040675726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 371.25 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map dsDNA-D2-I complex

Fileemd_50355_additional_1.map
AnnotationSharpened map dsDNA-D2-I complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 dsDNA-D2-I complex

Fileemd_50355_half_map_1.map
AnnotationHalf map 1 dsDNA-D2-I complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 dsDNA-D2-I complex

Fileemd_50355_half_map_2.map
AnnotationHalf map 2 dsDNA-D2-I complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dsDNA-FANCD2-FANCI complex

EntireName: dsDNA-FANCD2-FANCI complex
Components
  • Complex: dsDNA-FANCD2-FANCI complex
    • Protein or peptide: Fanconi anemia protein FANCD2
    • Protein or peptide: Fanconi anemia complementation group I
    • DNA: DNA (32-MER)
    • DNA: DNA (33-MER)

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Supramolecule #1: dsDNA-FANCD2-FANCI complex

SupramoleculeName: dsDNA-FANCD2-FANCI complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 310 MDa

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Macromolecule #1: Fanconi anemia protein FANCD2

MacromoleculeName: Fanconi anemia protein FANCD2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 164.731344 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSKRKLSKI DAAEESSKTD LQSRCPETKR SRISDKRAPS QGGLENEGVF EELLRTSGII LKVGEGQNEI AVDQTAFQKK LRVALEKHP SYPGVVNEFI SGLESHIKDR SQFKNCLLPC TPARTEGSRT LVHSYCESLI KLLLGIKILQ PAVVTLLLEK I PEFFFDVV ...String:
MVSKRKLSKI DAAEESSKTD LQSRCPETKR SRISDKRAPS QGGLENEGVF EELLRTSGII LKVGEGQNEI AVDQTAFQKK LRVALEKHP SYPGVVNEFI SGLESHIKDR SQFKNCLLPC TPARTEGSRT LVHSYCESLI KLLLGIKILQ PAVVTLLLEK I PEFFFDVV GTFGTNFPRL IVNQFKWLDG LLDSQDLVKK LMQMLSVSPV PIQHDIITSL PEILEDSQQN EVARELSCLL KQ GRRLTVP ILDALSRLDL DAELLAKVRQ SAMTIVPSVK LEDLPVVIKF ILHNVKAADA VEVISDLRKS LDLSSCVLPL QLL GSQRKL KSQAQASSSM SQVTTSQNCV KLLFDVIKLA VRFQKDVSEA WIKAIENSTS VSDHKVLDLI VLLLIHSTNS KNRK QTEKV LRSKIRLGCM PEQLMQNAFQ NHSMVIKDFF PSILSLAQTF LHSAHPAVVS FGSCMYKQAF AVFDSYCQQE VVCAL VTHV CSGNETELDI SLDVLTDLVI LHPSLLLRYA TFVKTILDSM QKLNPCQIRK LFYILSTLAF SQRQEGSYIQ DDMHMV IRK WLSSSVPNHK QMGIIGAVTM MGSVALKRNE ADGGLLERPE LSIECDGQLS TLLDLVGFCC EQTPEVLALY YDELANL IE KQKGNLDLQL LDKFGKSLVE DFPNDFVVDL SPTVDGSFLF PVKSLYNLDE DETQGAIAIN LLPLVSQSEP GRVADEMS N SRKRVVSPIC LSPCFRLLRL YTGEQNNGSL EEIDALLGCP LYLTDLEVEG KLDSLSKQER EFLCSLLFYA LNWFREVVN AFCQQQDAEM KGKVLTRLQN ITELQNVLGK CLAATPGYVP PPATFDSEAP EGVPSINAGG PVRKKNGKKR KSDSSKACSA ERTQADESS DGNQPDTELS ELEKSAAEKE TGNPLAQLQS YRPYFRELDL EVFSVLHCGL LTKSILDTEM HTEASEVVQL G PAELCFLL DDMCWKLEHV LTPGSTRRVP FLKERGNKDV GFSHLCQRSP KEVAVCVVKL LKPLCNHMEN MHNYFQTVIP NQ GVVDESG LNIQEYQLMS SCYHQLLLAF RLLFAWSGFS QHENSNLLRS ALQVLADRLK PGETEFLPLE ELISESFQYL LNF QASIPS FQCAFILTQV LMAISEKPMT GWKREKMASL AKQFLCQSWM KPGGDREKGS HFNSALHTLL CVYLEHTDNI LKAI EEISS VGVPELINSA KDGCSSTYPT LSRQTFPVFF RVMMAQLESS VKSIPAGKPS DSGEVQLEKL LKWNIAVRNF HILIN LVKV FDSRPVLSIC LKYGRLFVEA FLKLAMPLLD HSFKKHRDDV QSLLKTLQLS TRQLHHMCGH SKIHQDLGLT NHVPLL KKS LEQFVYRVKA MLAFNHCQEA FWVGVLKNRD LQGEEILSQA SAAPEEDSAE GSEEDTEDSA AEEPDGTDSD SGGAGRL EV LFQGPWSHPQ FEKGSAGSAA GSGAGWSHPQ FEK

UniProtKB: Fanconi anemia protein FANCD2

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Macromolecule #2: Fanconi anemia complementation group I

MacromoleculeName: Fanconi anemia complementation group I / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 149.458297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAQRILQLAA EGSPERLQEA LQGLTEGELG DMVTRQALRG RETAALLKGI FKGSPCSQQS GVLRRLQVYK HCVSLVESGD LHVGKVSEI IGLLMLEARQ LPGHALAELA TLFVEVIKRG SLSNGKSLEL FSTVLTALSN SKESLAYGKG ELNGEEFKKQ L INTLCSSK ...String:
MAQRILQLAA EGSPERLQEA LQGLTEGELG DMVTRQALRG RETAALLKGI FKGSPCSQQS GVLRRLQVYK HCVSLVESGD LHVGKVSEI IGLLMLEARQ LPGHALAELA TLFVEVIKRG SLSNGKSLEL FSTVLTALSN SKESLAYGKG ELNGEEFKKQ L INTLCSSK WDPQCVIHLA NMFRDIPLSG EELQFVVEKV LRMFSKLDLQ EIPPLVYQLL LLSAKGSKKT VLEGIISFFN QL DKRQKEE QRVPQSADLE VATVPLDQLR HVEGTVILHI VSAINLDQDI GEELIKHLKT EQQKDPGKAL CPFSVSLLLS TAV KHRLQE QIFDFLKTSI TRSCKDLQIL QASKFLQDLC PQQYDVTAVI LEVVKNSAFG WDHVTQGLVD LGFSLMESYE PKKS FGGKA AETNLGLSKM PAQQACKLGA SILLETFKVH EPIRSDILEQ VLNRVLTKAA SPVSHFIDLL SNIVVSAPLV LQNSS SRVT ETFDNLSFLP IDTVQGLLRA VQPLLKVSMS VRDSLILVLQ KAIFSRQLDA RKAAVAGFLL LLRNFKILGS LTSSQC SQA IGATQVQADV HACYNSAANE AFCLEILGSL RRCLSQQADV RLMLYEGFYD VLRRNSQLAS SIMETLLSQI KQYYLPQ QD LLPPLKLEGC IMAQGDQIFL QEPLAHLLCC IQHCLAWYKS TVHLCKGAED EEEEEDVGFE QNFEEMLESV TRRMIKSE L EDFELDKSAD FSPSSGVGVK NNIYAIQVMG ICEVLIEYNF KIGNFSKNKF EDVLGLFTCY NKLSEILKEK AGKNKSTLG NRIARSFLSM GFVSTLLTAL FRDNAQSHEE SLAVLRSSTE FMRYAVSVAL QKVQQLEEMG QTDGPDGQNP EKMFQNLCKI TRVLLWRYT SIPTAVEESG KKKGKSISLL CLEGLLRIFN TMQQLYAARI PQFLQALDIT DGDAEEADIN VTEKAAFQIR Q FQRSLVNQ LSSAEDDFNS KETQLLITIL STLSKLLDPG SQQFLQFLTW TVKICKENAL EDLSCCKGLL TLLFSLHVLY KS PVSLLRE LAQDIHACLG DIDQDVEIES RSHFAIVNVK TAAPTVCLLV LGQADKVLEE VDWLIKRLTI LGSDTSEDST QAS NQTQAL EKGVILQLGT LLTVFHELVQ TALPAGSCVD SLLRSLSKTY AILTSLIKHY IQACRSTSNT VPGRLEKLVK LSGS HLTPQ CYSFITYVQN IHSESLSFAE EKKKKKKEDE TAVVSTVMAK VLRDTKPIPN LIFAIEQYEK FLIHLSKKSK VNLMQ YMKL STSRDFRINA SMLDSVLQEQ NTEDAENEPD NNQSGTAEQP DENQEPQKKR RRKK

UniProtKB: Fanconi anemia complementation group I

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Macromolecule #3: DNA (32-MER)

MacromoleculeName: DNA (32-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.891366 KDa
SequenceString:
(DG)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DT)(DT) (DC)(DA)(DG)(DA)(DG)(DC)(DA)(DG)(DG)(DC) (DG)(DT)(DT)(DC)(DC)(DG)(DT)(DT)(DC) (DA)(DA)(DA)

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Macromolecule #4: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.133539 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DG)(DA)(DA)(DC)(DG)(DG) (DA)(DA)(DC)(DG)(DC)(DC)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DA)(DA)(DC)(DC)(DT)(DG) (DT)(DG)(DC)(DC)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initial model generated in RELION 4.0
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 165469
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)

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