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- EMDB-50353: ss-dsDNA-FANCD2-FANCI complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50353
Titless-dsDNA-FANCD2-FANCI complex
Map dataConsensus map of ss-dsDNA-D2-I complex
Sample
  • Complex: ss-dsDNA-FANCD2-FANCI complex
    • DNA: DNA (5'-D(P*GP*CP*AP*GP*CP*TP*GP*TP*CP*TP*AP*GP*AP*GP*AP*CP*AP*TP*CP*GP*AP*T)-3')
    • DNA: DNA (5'-D(P*CP*GP*AP*TP*GP*TP*CP*TP*CP*TP*AP*GP*AP*CP*AP*GP*CP*TP*GP*C)-3')
    • Protein or peptide: Fanconi anemia protein FANCD2
    • Protein or peptide: Fanconi anemia complementation group I
Keywordsss-dsDNA-FANCD2-FANCI / Fanconi Anemia / D2-I complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


Fanconi Anemia Pathway in DNA repair / double-strand break repair involved in meiotic recombination / homologous chromosome pairing at meiosis / mitotic intra-S DNA damage checkpoint signaling / interstrand cross-link repair / DNA polymerase binding / condensed chromosome / 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: 3.59 Å
AuthorsAlcon P / Passmore LA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105192715 United Kingdom
CitationJournal: To Be Published
Title: ss-dsDNA-FANCD2-FANCI complex
Authors: Alcon P / Passmore LA
History
DepositionMay 22, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50353.png

Downloads & links

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Map

FileDownload / File: emd_50353.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map of ss-dsDNA-D2-I complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.85 Å		0.83 Å/pix.
x 350 pix.
= 290.85 Å		0.83 Å/pix.
x 350 pix.
= 290.85 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.0076376903 - 0.013592266
Average (Standard dev.)0.000018380653 (±0.00043046757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.84998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of ss-dsDNA-D2-I complex

Fileemd_50353_additional_1.map
AnnotationSharpened map of ss-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 of ss-dsDNA-D2-I complex

Fileemd_50353_half_map_1.map
AnnotationHalf map 1 of ss-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 of ss-dsDNA-D2-I complex

Fileemd_50353_half_map_2.map
AnnotationHalf map 2 of ss-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 : ss-dsDNA-FANCD2-FANCI complex

EntireName: ss-dsDNA-FANCD2-FANCI complex
Components
  • Complex: ss-dsDNA-FANCD2-FANCI complex
    • DNA: DNA (5'-D(P*GP*CP*AP*GP*CP*TP*GP*TP*CP*TP*AP*GP*AP*GP*AP*CP*AP*TP*CP*GP*AP*T)-3')
    • DNA: DNA (5'-D(P*CP*GP*AP*TP*GP*TP*CP*TP*CP*TP*AP*GP*AP*CP*AP*GP*CP*TP*GP*C)-3')
    • Protein or peptide: Fanconi anemia protein FANCD2
    • Protein or peptide: Fanconi anemia complementation group I

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Supramolecule #1: ss-dsDNA-FANCD2-FANCI complex

SupramoleculeName: ss-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: DNA (5'-D(P*GP*CP*AP*GP*CP*TP*GP*TP*CP*TP*AP*GP*AP*GP*AP*CP*AP*TP...

MacromoleculeName: DNA (5'-D(P*GP*CP*AP*GP*CP*TP*GP*TP*CP*TP*AP*GP*AP*GP*AP*CP*AP*TP*CP*GP*AP*T)-3')
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.776392 KDa
SequenceString:
(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT) (DA)(DG)(DA)(DG)(DA)(DC)(DA)(DT)(DC)(DG) (DA)(DT)

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Macromolecule #2: DNA (5'-D(P*CP*GP*AP*TP*GP*TP*CP*TP*CP*TP*AP*GP*AP*CP*AP*GP*CP*TP...

MacromoleculeName: DNA (5'-D(P*CP*GP*AP*TP*GP*TP*CP*TP*CP*TP*AP*GP*AP*CP*AP*GP*CP*TP*GP*C)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.109954 KDa
SequenceString:
(DC)(DG)(DA)(DT)(DG)(DT)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DG)(DC)

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Macromolecule #3: Fanconi anemia protein FANCD2

MacromoleculeName: Fanconi anemia protein FANCD2 / type: protein_or_peptide / ID: 3 / 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 #4: Fanconi anemia complementation group I

MacromoleculeName: Fanconi anemia complementation group I / type: protein_or_peptide / ID: 4 / 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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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: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 319378
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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