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- EMDB-23086: Structure of the human Fanconi anaemia Core-ID complex -

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Basic information

Entry
Database: EMDB / ID: EMD-23086
TitleStructure of the human Fanconi anaemia Core-ID complex
Map datacomposite REFMAC5 map (masked) used in coordinate refinement
Sample
  • Complex: Human Fanconi Anaemia Core-ID complex
    • Protein or peptide: x 11 types
  • Ligand: x 1 types
KeywordsComplex / LIGASE
Function / homology
Function and homology information


regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance ...regulation of germ cell proliferation / regulation of CD40 signaling pathway / Fanconi anaemia nuclear complex / regulation of regulatory T cell differentiation / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / male meiotic nuclear division / gamete generation / replication-born double-strand break repair via sister chromatid exchange / neuronal stem cell population maintenance / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / myeloid cell homeostasis / negative regulation of double-strand break repair via homologous recombination / positive regulation of double-strand break repair via homologous recombination / female gonad development / protein monoubiquitination / spermatid development / germ cell development / removal of superoxide radicals / interstrand cross-link repair / DNA polymerase binding / ovarian follicle development / condensed chromosome / mitochondrion organization / nucleotide-excision repair / Fanconi Anemia Pathway / response to gamma radiation / TP53 Regulates Transcription of DNA Repair Genes / RING-type E3 ubiquitin transferase / response to radiation / PKR-mediated signaling / ubiquitin-protein transferase activity / male gonad development / ubiquitin protein ligase activity / cellular response to oxidative stress / nuclear envelope / chromosome / regulation of cell population proliferation / regulation of inflammatory response / protein-containing complex assembly / damaged DNA binding / nuclear body / DNA repair / intracellular membrane-bounded organelle / centrosome / DNA damage response / ubiquitin protein ligase binding / chromatin / nucleolus / mitochondrion / DNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein ...Fanconi anaemia group C protein / Fanconi anemia-associated protein of 100kDa / Fanconi anemia group B protein / Fanconi anemia group G protein / Fanconi anaemia group C protein / Fanconi anemia-associated / Fanconi Anaemia group E protein, C-terminal / Fanconi anemia group F protein / FANCF, C-terminal domain superfamily / Fanconi anemia group E protein / Fanconi anemia group F protein (FANCF) / Fanconi Anaemia group E protein FANCE / Fanconi anaemia group A protein / Fanconi anaemia group A protein, N-terminal domain / Fanconi anaemia group A protein / Fanconi anaemia group A protein N terminus / FANCL, UBC-like domain 2 / FANCL, UBC-like domain 3 / Fanconi anemia complex, subunit FancL, WD-repeat containing domain / E3 ubiquitin-protein ligase FANCL / FANCL C-terminal domain / FANCL, UBC-like domain 3 superfamily / FANCL UBC-like domain 1 / FANCL C-terminal domain / FANCL UBC-like domain 2 / FANCL UBC-like domain 3 / FANCL C-terminal domain / 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 / Ubiquitin-conjugating enzyme/RWD-like / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Fanconi anemia, complementation group I / Fanconi anemia group G protein / Fanconi anemia group A protein / Fanconi anemia group C protein / Fanconi anemia core complex-associated protein 100 / Fanconi anemia group B protein / Fanconi anemia group D2 protein / Fanconi anemia group E protein / Fanconi anemia group F protein / E3 ubiquitin-protein ligase FANCL
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang SL / Pavletich NP
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structure of the FA core ubiquitin ligase closing the ID clamp on DNA.
Authors: Shengliu Wang / Renjing Wang / Christopher Peralta / Ayat Yaseen / Nikola P Pavletich /
Abstract: The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates ...The Fanconi anemia (FA) pathway is essential for the repair of DNA interstrand crosslinks. Central to the pathway is the FA core complex, a ubiquitin ligase of nine subunits that monoubiquitinates the FANCI-FANCD2 (ID) DNA clamp. The 3.1 Å structure of the 1.1-MDa human FA core complex, described here, reveals an asymmetric assembly with two copies of all but the FANCC, FANCE and FANCF subunits. The asymmetry is crucial, as it prevents the binding of a second FANCC-FANCE-FANCF subcomplex that inhibits the recruitment of the UBE2T ubiquitin conjugating enzyme, and instead creates an ID binding site. A single active site then ubiquitinates FANCD2 and FANCI sequentially. We also present the 4.2-Å structures of the human core-UBE2T-ID-DNA complex in three conformations captured during monoubiquitination. They reveal the core-UBE2T complex remodeling the ID-DNA complex, closing the clamp on the DNA before ubiquitination. Monoubiquitination then prevents clamp opening after release from the core.
History
DepositionDec 10, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kzq
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23086.png

Downloads & links

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Map

FileDownload / File: emd_23086.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite REFMAC5 map (masked) used in coordinate refinement
Voxel sizeX=Y=Z: 1.08847 Å
Density
Contour LevelBy AUTHOR: 0.0055 / Movie #1: 0.0055
Minimum - Maximum-0.039199647 - 0.07067928
Average (Standard dev.)0.0000022401216 (±0.0013053681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 487.63455 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.08847098214291.08847098214291.0884709821429
M x/y/z448448448
origin x/y/z0.0000.0000.000
length x/y/z487.635487.635487.635
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS448448448
D min/max/mean-0.0390.0710.000

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Supplemental data

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Additional map: consensus reconstruction postprocessed with relion

Fileemd_23086_additional_1.map
Annotationconsensus reconstruction postprocessed with relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focus1: reconstruction (masked) focused at FANCC-Entd-F-L-G and FANCB-FAAP100...

Fileemd_23086_additional_2.map
Annotationfocus1: reconstruction (masked) focused at FANCC-Entd-F-L-G and FANCB-FAAP100 dimer of heterodimers postprocessed with relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focus2: reconstruction (masked) focused at FANCA-A'dimer with relion

Fileemd_23086_additional_3.map
Annotationfocus2: reconstruction (masked) focused at FANCA-A'dimer with relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: focus3: reconstruction (masked) focused at FANCA' NTD, FANCG',...

Fileemd_23086_additional_4.map
Annotationfocus3: reconstruction (masked) focused at FANCA' NTD, FANCG', FANCB-FAAP100 dimer of heterodimers, FANCEctd, FANCL' and the ID complex postprocessed with relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Fanconi Anaemia Core-ID complex

EntireName: Human Fanconi Anaemia Core-ID complex
Components
  • Complex: Human Fanconi Anaemia Core-ID complex
    • Protein or peptide: Fanconi anemia group A protein
    • Protein or peptide: Fanconi anemia group B protein
    • Protein or peptide: Fanconi anemia group C protein
    • Protein or peptide: Fanconi anemia group E protein
    • Protein or peptide: Fanconi anemia group F protein
    • Protein or peptide: Fanconi anemia group G protein
    • Protein or peptide: E3 ubiquitin-protein ligase FANCL
    • Protein or peptide: Fanconi anemia core complex-associated protein 100
    • Protein or peptide: Fanconi anemia core complex-associated protein 20
    • Protein or peptide: Fanconi anemia, complementation group I
    • Protein or peptide: Fanconi anemia group D2 protein
  • Ligand: ZINC ION

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Supramolecule #1: Human Fanconi Anaemia Core-ID complex

SupramoleculeName: Human Fanconi Anaemia Core-ID complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.1 MDa

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Macromolecule #1: Fanconi anemia group A protein

MacromoleculeName: Fanconi anemia group A protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 165.513016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSDSWVPNSA SGQDPGGRRR AWAELLAGRV KREKYNPERA QKLKESAVRL LRSHQDLNAL LLEVEGPLCK KLSLSKVIDC DSSEAYANH SSSFIGSALQ DQASRLGVPV GILSAGMVAS SVGQICTAPA ETSHPVLLTV EQRKKLSSLL EFAQYLLAHS M FSRLSFCQ ...String:
MSDSWVPNSA SGQDPGGRRR AWAELLAGRV KREKYNPERA QKLKESAVRL LRSHQDLNAL LLEVEGPLCK KLSLSKVIDC DSSEAYANH SSSFIGSALQ DQASRLGVPV GILSAGMVAS SVGQICTAPA ETSHPVLLTV EQRKKLSSLL EFAQYLLAHS M FSRLSFCQ ELWKIQSSLL LEAVWHLHVQ GIVSLQELLE SHPDMHAVGS WLFRNLCCLC EQMEASCQHA DVARAMLSDF VQ MFVLRGF QKNSDLRRTV EPEKMPQVTV DVLQRMLIFA LDALAAGVQE ESSTHKIVRC WFGVFSGHTL GSVISTDPLK RFF SHTLTQ ILTHSPVLKA SDAVQMQREW SFARTHPLLT SLYRRLFVML SAEELVGHLQ EVLETQEVHW QRVLSFVSAL VVCF PEAQQ LLEDWVARLM AQAFESCQLD SMVTAFLVVR QAALEGPSAF LSYADWFKAS FGSTRGYHGC SKKALVFLFT FLSEL VPFE SPRYLQVHIL HPPLVPGKYR SLLTDYISLA KTRLADLKVS IENMGLYEDL SSAGDITEPH SQALQDVEKA IMVFEH TGN IPVTVMEASI FRRPYYVSHF LPALLTPRVL PKVPDSRVAF IESLKRADKI PPSLYSTYCQ ACSAAEEKPE DAALGVR AE PNSAEEPLGQ LTAALGELRA SMTDPSQRDV ISAQVAVISE RLRAVLGHNE DDSSVEISKI QLSINTPRLE PREHMAVD L LLTSFCQNLM AASSVAPPER QGPWAALFVR TMCGRVLPAV LTRLCQLLRH QGPSLSAPHV LGLAALAVHL GESRSALPE VDVGPPAPGA GLPVPALFDS LLTCRTRDSL FFCLKFCTAA ISYSLCKFSS QSRDTLCSCL SPGLIKKFQF LMFRLFSEAR QPLSEEDVA SLSWRPLHLP SADWQRAALS LWTHRTFREV LKEEDVHLTY QDWLHLELEI QPEADALSDT ERQDFHQWAI H EHFLPESS ASGGCDGDLQ AACTILVNAL MDFHQSSRSY DHSENSDLVF GGRTGNEDII SRLQEMVADL ELQQDLIVPL GH TPSQEHF LFEIFRRRLQ ALTSGWSVAA SLQRQRELLM YKRILLRLPS SVLCGSSFQA EQPITARCEQ FFHLVNSEMR NFC SHGGAL TQDITAHFFR GLLNACLRSR DPSLMVDFIL AKCQTKCPLI LTSALVWWPS LEPVLLCRWR RHCQSPLPRE LQKL QEGRQ FASDFLSPEA ASPAPNPDWL SAAALHFAIQ QVREENIRKQ LKKLDCEREE LLVFLFFFSL MGLLSSHLTS NSTTD LPKA FHVCAAILEC LEKRKISWLA LFQLTESDLR LGRLLLRVAP DQHTRLLPFA FYSLLSYFHE DAAIREEAFL HVAVDM YLK LVQLFVAGDT STVSPPAGRS LELKGQGNPV ELITKARLFL LQLIPRCPKK SFSHVAELLA DRGDCDPEVS AALQSRQ QA APDADLSQEP HLFAAAKLVD EDLYFQSDYK DDDDK

UniProtKB: Fanconi anemia group A protein

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Macromolecule #2: Fanconi anemia group B protein

MacromoleculeName: Fanconi anemia group B protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.640172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRK LGTGSMTSKQ AMSSNEQERL LCYNGEVLVF QLSKGNFADK EPTKTPILHV RRMVFDRGTK VFVQKSTGF FTIKEENSHL KIMCCNCVSD FRTGINLPYI VIEKNKKNNV FEYFLLILHS TNKFEMRLSF KLGYEMKDGL R VLNGPLIL ...String:
MDYKDDDDKE NLYFQGGGRK LGTGSMTSKQ AMSSNEQERL LCYNGEVLVF QLSKGNFADK EPTKTPILHV RRMVFDRGTK VFVQKSTGF FTIKEENSHL KIMCCNCVSD FRTGINLPYI VIEKNKKNNV FEYFLLILHS TNKFEMRLSF KLGYEMKDGL R VLNGPLIL WRHVKAFFFI SSQTGKVVSV SGNFSSIQWA GEIENLGMVL LGLKECCLSE EECTQEPSKS DYAIWNTKFC VY SLESQEV LSDIYIIPPA YSSVVTYVHI CATEIIKNQL RISLIALTRK NQLISFQNGT PKNVCQLPFG DPCAVQLMDS GGG NLFFVV SFISNNACAV WKESFQVAAK WEKLSLVLID DFIGSGTEQV LLLFKDSLNS DCLTSFKITD LGKINYSSEP SDCN EDDLF EDKQENRYLV VPPLETGLKV CFSSFRELRQ HLLLKEKIIS KSYKALINLV QGKDDNTSSA EEKECLVPLC GEEEN SVHI LDEKLSDNFQ DSEQLVEKIW YRVIDDSLVV GVKTTSSLKL SLNDVTLSLL MDQAHDSRFR LLKCQNRVIK LSTNPF PAP YLMPCEIGLE AKRVTLTPDS KKEESFVCEH PSKKECVQII TAVTSLSPLL TFSKFCCTVL LQIMERESGN CPKDRYV VC GRVFLSLEDL STGKYLLTFP KKKPIEHMED LFALLAAFHK SCFQITSPGY ALNSMKVWLL EHMKCEIIKE FPEVYFCE R PGSFYGTLFT WKQRTPFEGI LIIYSRNQTV MFQCLHNLIR ILPINCFLKN LKSGSENFLI DNMAFTLEKE LVTLSSLSS AIAKHESNFM QRCEVSKGKS SVVAAALSDR RENIHPYRKE LQREKKKMLQ TNLKVSGALY REITLKVAEV QLKSDFAAQK LSNL

UniProtKB: Fanconi anemia group B protein

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Macromolecule #3: Fanconi anemia group C protein

MacromoleculeName: Fanconi anemia group C protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.290359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRK LGTGSMAQDS VDLSCDYQFW MQKLSVWDQA STLETQQDTC LHVAQFQEFL RKMYEALKEM DSNTVIERF PTIGQLLAKA CWNPFILAYD ESQKILIWCL CCLINKEPQN SGQSKLNSWI QGVLSHILSA LRFDKEVALF T QGLGYAPI ...String:
MDYKDDDDKE NLYFQGGGRK LGTGSMAQDS VDLSCDYQFW MQKLSVWDQA STLETQQDTC LHVAQFQEFL RKMYEALKEM DSNTVIERF PTIGQLLAKA CWNPFILAYD ESQKILIWCL CCLINKEPQN SGQSKLNSWI QGVLSHILSA LRFDKEVALF T QGLGYAPI DYYPGLLKNM VLSLASELRE NHLNGFNTQR RMAPERVASL SRVCVPLITL TDVDPLVEAL LICHGREPQE IL QPEFFEA VNEAILLKKI SLPMSAVVCL WLRHLPSLEK AMLHLFEKLI SSERNCLRRI ECFIKDSSLP QAACHPAIFR VVD EMFRCA LLETDGALEI IATIQVFTQC FVEALEKASK QLRFALKTYF PYTSPSLAMV LLQDPQDIPR GHWLQTLKHI SELL REAVE DQTHGSCGGP FESWFLFIHF GGWAEMVAEQ LLMSAAEPPT ALLWLLAFYY GPRDGRQQRA QTMVQVKAVL GHLLA MSRS SSLSAQDLQT VAGQGTDTDL RAPAQQLIRH LLLNFLLWAP GGHTIAWDVI TLMAHTAEIT HEIIGFLDQT LYRWNR LGI ESPRSEKLAR ELLKELRTQV

UniProtKB: Fanconi anemia group C protein

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Macromolecule #4: Fanconi anemia group E protein

MacromoleculeName: Fanconi anemia group E protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.026086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRM ATPDAGLPGA EGVEPAPWAQ LEAPARLLLQ ALQAGPEGAR RGLGVLRALG SRGWEPFDWG RLLEALCRE EPVVQGPDGR LELKPLLLRL PRICQRNLMS LLMAVRPSLP ESGLLSVLQI AQQDLAPDPD AWLRALGELL R RDLGVGTS ...String:
MDYKDDDDKE NLYFQGGGRM ATPDAGLPGA EGVEPAPWAQ LEAPARLLLQ ALQAGPEGAR RGLGVLRALG SRGWEPFDWG RLLEALCRE EPVVQGPDGR LELKPLLLRL PRICQRNLMS LLMAVRPSLP ESGLLSVLQI AQQDLAPDPD AWLRALGELL R RDLGVGTS MEGASPLSER CQRQLQSLCR GLGLGGRRLK SPQAPDPEEE ENRDSQQPGK RRKDSEEEAA SPEGKRVPKR LR CWEEEED HEKERPEHKS LESLADGGSA SPIKDQPVMA VKTGEDGSNL DDAKGLAESL ELPKAIQDQL PRLQQLLKTL EEG LEGLED APPVELQLLH ECSPSQMDLL CAQLQLPQLS DLGLLRLCTW LLALSPDLSL SNATVLTRSL FLGRILSLTS SASR LLTTA LTSFCAKYTY PVCSALLDPV LQAPGTGPAQ TELLCCLVKM ESLEPDAQVL MLGQILELPW KEETFLVLQS LLERQ VEMT PEKFSVLMEK LCKKGLAATT SMAYAKLMLT VMTKYQANIT ETQRLGLAMA LEPNTTFLRK SLKAALKHLG P

UniProtKB: Fanconi anemia group E protein

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Macromolecule #5: Fanconi anemia group F protein

MacromoleculeName: Fanconi anemia group F protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.108297 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRK LGTGSMESLL QHLDRFSELL AVSSTTYVST WDPATVRRAL QWARYLRHIH RRFGRHGPIR TALERRLHN QWRQEGGFGR GPVPGLANFQ ALGHCDVLLS LRLLENRALG DAARYHLVQQ LFPGPGVRDA DEETLQESLA R LARRRSAV ...String:
MDYKDDDDKE NLYFQGGGRK LGTGSMESLL QHLDRFSELL AVSSTTYVST WDPATVRRAL QWARYLRHIH RRFGRHGPIR TALERRLHN QWRQEGGFGR GPVPGLANFQ ALGHCDVLLS LRLLENRALG DAARYHLVQQ LFPGPGVRDA DEETLQESLA R LARRRSAV HMLRFNGYRE NPNLQEDSLM KTQAELLLER LQEVGKAEAE RPARFLSSLW ERLPQNNFLK VIAVALLQPP LS RRPQEEL EPGIHKSPGE GSQVLVHWLL GNSEVFAAFC RALPAGLLTL VTSRHPALSP VYLGLLTDWG QRLHYDLQKG IWV GTESQD VPWEELHNRF QSLCQAPPPL KDKVLTALET CKAQDGDFEV PGLSIWTDLL LALRSGAFRK RQVLGLSAGL SSV

UniProtKB: Fanconi anemia group F protein

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Macromolecule #6: Fanconi anemia group G protein

MacromoleculeName: Fanconi anemia group G protein / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.873727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRM SRQTTSVGSS CLDLWREKND RLVRQAKVAQ NSGLTLRRQQ LAQDALEGLR GLLHSLQGLP AAVPVLPLE LTVTCNFIIL RASLAQGFTE DQAQDIQRSL ERVLETQEQQ GPRLEQGLRE LWDSVLRASC LLPELLSALH R LVGLQAAL ...String:
MDYKDDDDKE NLYFQGGGRM SRQTTSVGSS CLDLWREKND RLVRQAKVAQ NSGLTLRRQQ LAQDALEGLR GLLHSLQGLP AAVPVLPLE LTVTCNFIIL RASLAQGFTE DQAQDIQRSL ERVLETQEQQ GPRLEQGLRE LWDSVLRASC LLPELLSALH R LVGLQAAL WLSADRLGDL ALLLETLNGS QSGASKDLLL LLKTWSPPAE ELDAPLTLQD AQGLKDVLLT AFAYRQGLQE LI TGNPDKA LSSLHEAASG LCPRPVLVQV YTALGSCHRK MGNPQRALLY LVAALKEGSA WGPPLLEASR LYQQLGDTTA ELE SLELLV EALNVPCSSK APQFLIEVEL LLPPPDLASP LHCGTQSQTK HILASRCLQT GRAGDAAEHY LDLLALLLDS SEPR FSPPP SPPGPCMPEV FLEAAVALIQ AGRAQDALTL CEELLSRTSS LLPKMSRLWE DARKGTKELP YCPLWVSATH LLQGQ AWVQ LGAQKVAISE FSRCLELLFR ATPEEKEQGA AFNCEQGCKS DAALQQLRAA ALISRGLEWV ASGQDTKALQ DFLLSV QMC PGNRDTYFHL LQTLKRLDRR DEATALWWRL EAQTKGSHED ALWSLPLYLE SYLSWIRPSD RDAFLEEFRT SLPKSCD L

UniProtKB: Fanconi anemia group G protein

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Macromolecule #7: E3 ubiquitin-protein ligase FANCL

MacromoleculeName: E3 ubiquitin-protein ligase FANCL / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.203953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKE NLYFQGGGRM AVTEASLLRQ CPLLLPQNRS KTVYEGFISA QGRDFHLRIV LPEDLQLKNA RLLCSWQLRT ILSGYHRIV QQRMQHSPDL MSFMMELKML LEVALKNRQE LYALPPPPQF YSSLIEEIGT LGWDKLVYAD TCFSTIKLKA E DASGREHL ...String:
MDYKDDDDKE NLYFQGGGRM AVTEASLLRQ CPLLLPQNRS KTVYEGFISA QGRDFHLRIV LPEDLQLKNA RLLCSWQLRT ILSGYHRIV QQRMQHSPDL MSFMMELKML LEVALKNRQE LYALPPPPQF YSSLIEEIGT LGWDKLVYAD TCFSTIKLKA E DASGREHL ITLKLKAKYP AESPDYFVDF PVPFCASWTP QSSLISIYSQ FLAAIESLKA FWDVMDEIDE KTWVLEPEKP PR SATARRI ALGNNVSINI EVDPRHPTML PECFFLGADH VVKPLGIKLS RNIHLWDPEN SVLQNLKDVL EIDFPARAIL EKS DFTMDC GICYAYQLDG TIPDQVCDNS QCGQPFHQIC LYEWLRGLLT SRQSFNIIFG ECPYCSKPIT LKMSGRKH

UniProtKB: E3 ubiquitin-protein ligase FANCL

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Macromolecule #8: Fanconi anemia core complex-associated protein 100

MacromoleculeName: Fanconi anemia core complex-associated protein 100 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.513898 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKGSMAGAA PRVRYLAGFC CPLGGLAAGK PRVLCHEAEV FLSTGSELVY VYDQEGGLLT AAFRFPDQV WHLELLAPRR LLYALCARRG LYCLSLDHPG RSRSTSQDDR DSEDGDQPSP VIPVDPDACI LPDAALCAFT L LDSVLVTL ...String:
MDYKDHDGDY KDHDIDYKDD DDKGSMAGAA PRVRYLAGFC CPLGGLAAGK PRVLCHEAEV FLSTGSELVY VYDQEGGLLT AAFRFPDQV WHLELLAPRR LLYALCARRG LYCLSLDHPG RSRSTSQDDR DSEDGDQPSP VIPVDPDACI LPDAALCAFT L LDSVLVTL VQGPARWKMQ LFEQPCPGED PRPGGQIGEV ELSSYTPPAG VPGKPAAPHF LPVLCSVSPS GSRVPHDLLG GS GGFTLED ALFGLLFGAD ATLLQSPVVL CGLPDGQLCC VILKALVTSR SAPGDPNALV KILHHLEEPV IFIGALKTEP QAA EAAENF LPDEDVHCDC LVAFGHHGRM LAIKASWDES GKLVPELREY CLPGPVLCAA CGGGGRVYHS TPSDLCVVDL SRGS TPLGP EQPEEGPGGL PPMLCPASLN ICSVVSLSAS PRTHEGGTKL LALSAKGRLM TCSLDLDSEM PGPARMTTES AGQKI KELL SGIGNISERV SFLKKAVDQR NKALTSLNEA MNVSCALLSS GTGPRPISCT TSTTWSRLQT QDVLMATCVL ENSSSF SLD QGWTLCIQVL TSSCALDLDS ACSAITYTIP VDQLGPGARR EVTLPLGPGE NGGLDLPVTV SCTLFYSLRE VVGGALA PS DSEDPFLDEC PSDVLPEQEG VCLPLSRHTV DMLQCLRFPG LAPPHTRAPS PLGPTRDPVA TFLETCREPG SQPAGPAS L RAEYLPPSVA SIKVSAELLR AALKDGHSGV PLCCATLQWL LAENAAVDVV RARALSSIQG VAPDGANVHL IVREVAMTD LCPAGPIQAV EIQVESSSLA DICRAHHAVV GRMQTMVTEQ ATQGSSAPDL RVQYLRQIHA NHETLLREVQ TLRDRLCTED EASSCATAQ RLLQVYRQLR HPSLILL

UniProtKB: Fanconi anemia core complex-associated protein 100

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Macromolecule #9: Fanconi anemia core complex-associated protein 20

MacromoleculeName: Fanconi anemia core complex-associated protein 20 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.041667 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)E PTEVFTVGPK TFSWTPFPPD LW(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #10: Fanconi anemia, complementation group I

MacromoleculeName: Fanconi anemia, complementation group I / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 149.512078 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA GTLRRRKIYT CCIQLVESGD LQKEIVSEI IGLLMLEAHH FPGPLLVELA NEFISAVREG SLVNGKSLEL LPIILTALAT KKENLAYGKG VLSGEECKKQ L INTLCSGR ...String:
MDQKILSLAA EKTADKLQEF LQTLREGDLT NLLQNQAVKG KVAGALLRAI FKGSPCSEEA GTLRRRKIYT CCIQLVESGD LQKEIVSEI IGLLMLEAHH FPGPLLVELA NEFISAVREG SLVNGKSLEL LPIILTALAT KKENLAYGKG VLSGEECKKQ L INTLCSGR WDQQYVIQLT SMFKDVPLTA EEVEFVVEKA LSMFSKMNLQ EIPPLVYQLL VLSSKGSRKS VLEGIIAFFS AL DKQHNEE QSGDELLDVV TVPSGELRHV EGTIILHIVF AIKLDYELGR ELVKHLKVGQ QGDSNNNLSP FSIALLLSVT RIQ RFQDQV LDLLKTSVVK SFKDLQLLQG SKFLQNLVPH RSYVSTMILE VVKNSVHSWD HVTQGLVELG FILMDSYGPK KVLD GKTIE TSPSLSRMPN QHACKLGANI LLETFKIHEM IRQEILEQVL NRVVTRASSP ISHFLDLLSN IVMYAPLVLQ SCSSK VTEA FDYLSFLPLQ TVQRLLKAVQ PLLKVSMSMR DCLILVLRKA MFANQLDARK SAVAGFLLLL KNFKVLGSLS SSQCSQ SLS VSQVHVDVHS HYNSVANETF CLEIMDSLRR CLSQQADVRL MLYEGFYDVL RRNSQLANSV MQTLLSQLKQ FYEPKPD LL PPLKLEACIL TQGDKISLQE PLDYLLCCIQ HCLAWYKNTV IPLQQGEEEE EEEEAFYEDL DDILESITNR MIKSELED F ELDKSADFSQ STSIGIKNNI SAFLVMGVCE VLIEYNFSIS SFSKNRFEDI LSLFMCYKKL SDILNEKAGK AKTKMANKT SDSLLSMKFV SSLLTALFRD SIQSHQESLS VLRSSNEFMR YAVNVALQKV QQLKETGHVS GPDGQNPEKI FQNLCDLTRV LLWRYTSIP TSVEESGKKE KGKSISLLCL EGLQKIFSAV QQFYQPKIQQ FLRALDVTDK EGEEREDADV SVTQRTAFQI R QFQRSLLN LLSSQEEDFN SKEALLLVTV LTSLSKLLEP SSPQFVQMLS WTSKICKENS REDALFCKSL MNLLFSLHVS YK SPVILLR DLSQDIHGHL GDIDQDVEVE KTNHFAIVNL RTAAPTVCLL VLSQAEKVLE EVDWLITKLK GQVSQETLSE EAS SQATLP NQPVEKAIIM QLGTLLTFFH ELVQTALPSG SCVDTLLKDL CKMYTTLTAL VRYYLQVCQS SGGIPKNMEK LVKL SGSHL TPLCYSFISY VQNKSKSLNY TGEKKEKPAV VATAMARVLR ETKPIPNLIF AIEQYEKFLI HLSKKSKVSL MQHMK LSTS RDFKIKGNIL DMVLREDGED ENEEGTASEH GGQNKEPAKK KRKK

UniProtKB: Fanconi anemia, complementation group I

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Macromolecule #11: Fanconi anemia group D2 protein

MacromoleculeName: Fanconi anemia group D2 protein / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 164.325516 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSKRRLSKS EDKESLTEDA SKTRKQPLSK KTKKSHIANE VEENDSIFVK LLKISGIILK TGESQNQLAV DQIAFQKKLF QTLRRHPSY PKIIEEFVSG LESYIEDEDS FRNCLLSCER LQDEEASMGA SYSKSLIKLL LGIDILQPAI IKTLFEKLPE Y FFENKNSD ...String:
MVSKRRLSKS EDKESLTEDA SKTRKQPLSK KTKKSHIANE VEENDSIFVK LLKISGIILK TGESQNQLAV DQIAFQKKLF QTLRRHPSY PKIIEEFVSG LESYIEDEDS FRNCLLSCER LQDEEASMGA SYSKSLIKLL LGIDILQPAI IKTLFEKLPE Y FFENKNSD EINIPRLIVS QLKWLDRVVD GKDLTTKIMQ LISIAPENLQ HDIITSLPEI LGDSQHADVG KELSDLLIEN TS LTVPILD VLSSLRLDPN FLLKVRQLVM DKLSSIRLED LPVIIKFILH SVTAMDTLEV ISELREKLDL QHCVLPSRLQ ASQ VKLKSK GRASSSGNQE SSGQSCIILL FDVIKSAIRY EKTISEAWIK AIENTASVSE HKVFDLVMLF IIYSTNTQTK KYID RVLRN KIRSGCIQEQ LLQSTFSVHY LVLKDMCSSI LSLAQSLLHS LDQSIISFGS LLYKYAFKFF DTYCQQEVVG ALVTH ICSG NEAEVDTALD VLLELVVLNP SAMMMNAVFV KGILDYLDNI SPQQIRKLFY VLSTLAFSKQ NEASSHIQDD MHLVIR KQL SSTVFKYKLI GIIGAVTMAG IMAADRSESP SLTQERANLS DEQCTQVTSL LQLVHSCSEQ SPQASALYYD EFANLIQ HE KLDPKALEWV GHTICNDFQD AFVVDSCVVP EGDFPFPVKA LYGLEEYDTQ DGIAINLLPL LFSQDFAKDG GPVTSQES G QKLVSPLCLA PYFRLLRLCV ERQHNGNLEE IDGLLDCPIF LTDLEPGEKL ESMSAKERSF MCSLIFLTLN WFREIVNAF CQETSPEMKG KVLTRLKHIV ELQIILEKYL AVTPDYVPPL GNFDVETLDI TPHTVTAISA KIRKKGKIER KQKTDGSKTS SSDTLSEEK NSECDPTPSH RGQLNKEFTG KEEKTSLLLH NSHAFFRELD IEVFSILHCG LVTKFILDTE MHTEATEVVQ L GPPELLFL LEDLSQKLES MLTPPIARRV PFLKNKGSRN IGFSHLQQRS AQEIVHCVFQ LLTPMCNHLE NIHNYFQCLA AE NHGVVDG PGVKVQEYHI MSSCYQRLLQ IFHGLFAWSG FSQPENQNLL YSALHVLSSR LKQGEHSQPL EELLSQSVHY LQN FHQSIP SFQCALYLIR LLMVILEKST ASAQNKEKIA SLARQFLCRV WPSGDKEKSN ISNDQLHALL CIYLEHTESI LKAI EEIAG VGVPELINSP KDASSSTFPT LTRHTFVVFF RVMMAELEKT VKKIEPGTAA DSQQIHEEKL LYWNMAVRDF SILIN LIKV FDSHPVLHVC LKYGRLFVEA FLKQCMPLLD FSFRKHREDV LSLLETFQLD TRLLHHLCGH SKIHQDTRLT QHVPLL KKT LELLVCRVKA MLTLNNCREA FWLGNLKNRD LQGEEIKSQN SQESTADESE DDMSSQASKS KATEDGEEDE VSAGEKE QD SDESYDDSD

UniProtKB: Fanconi anemia group D2 protein

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Macromolecule #12: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 12 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4Bicine
150.0 mMNaClSodium chloridesodium chloride
1.0 mMC4H10O2S2Dithiothreitol
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 65.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76111

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