2024-05-22 REL PDBe PDBe PDBe 2019-12-07 2020-02-19 2020-02-19 2024-05-22 Medical Research Council (MRC, United Kingdom) MC_U105192715 United Kingdom European Molecular Biology Organization (EMBO) ALTF 692-2018 United Kingdom Structure of monoubiquitinated FANCD2 in complex with FANCI and DNA Alcon P Shakeel S Fanconi anaemia, ubiquitin, DNA repair, DNA damage, inter-strand crosslink, DNA BINDING PROTEIN Alcon P Shakeel S Chen ZA Rappsilber J Patel KJ Passmore LA FANCD2-FANCI is a clamp stabilized on DNA by monoubiquitination of FANCD2 during DNA repair. Nat.Struct.Mol.Biol. US 27 240 248 2020 32066963 doi:10.1038/s41594-020-0380-1 1545-9985 6tnf FULLOVERLAP Complex of monoubiquitinated FANCD2, FANCI and DNA Complex of monoubiquitinated FANCD2, FANCI and DNA 0 1 2 3 4 0.3 FANCD2, FANCI 1 1 2 Gallus gallus UBC 1 3 Homo sapiens DNA 1 4
An idealized dsDNA of 33 bp of arbitrary sequence was placed and refined into the EM density but the following DNA sequences were used in the sample preparation by annealing oligonucleotides X1, X2, X3, X4, X5, X6: X1: GCGCACCAAGAGATACGCGGTCGAATGCCGAGTAGCCATCAGCG X2: ACCATGCAGCTACTCGGCATTCGACCGCGTATCTGGCGACTACG X3: TATCTCTTGGTGCGC X4: CGCTGATGGCTACTC X5: CGTAGTCGCCAGATA X6: GAGTAGCTGCATGGT
Synthetic construct FANCD2 Gallus gallus 0.160932328 1 Spodoptera frugiperda LEVO MVSKRKLSKIDAAEESSKTDLQSRCPETKRSRISDKRAPSQGGLENEGVFEELLRTSGIILKVGEGQNEIAVDQTAFQKK LRVALEKHPSYPGVVNEFISGLESHIKDRSQFKNCLLPCTPARTEGSRTLVHSYCESLIKLLLGIKILQPAVVTLLLEKI PEFFFDVVGTFGTNFPRLIVNQFKWLDGLLDSQDLVKKLMQMLSVSPVPIQHDIITSLPEILEDSQQNEVARELSCLLKQ GRRLTVPILDALSRLDLDAELLAKVRQSAMTIVPSVKLEDLPVVIKFILHNVKAADAVEVISDLRKSLDLSSCVLPLQLL GSQRKLKSQAQASSSMSQVTTSQNCVKLLFDVIKLAVRFQKDVSEAWIKAIENSTSVSDHKVLDLIVLLLIHSTNSKNRK QTEKVLRSKIRLGCMPEQLMQNAFQNHSMVIKDFFPSILSLAQTFLHSAHPAVVSFGSCMYKQAFAVFDSYCQQEVVCAL VTHVCSGNETELDISLDVLTDLVILHPSLLLRYATFVKTILDSMQKLNPCQIRKLFYILSTLAFSQRQEGSYIQDDMHMV IRKWLSSSVPNHKQMGIIGAVTMMGSVALKRNEADGGLLERPELSIECDGQLSTLLDLVGFCCEQTPEVLALYYDELANL IEKQKGNLDLQLLDKFGKSLVEDFPNDFVVDLSPTVDGSFLFPVKSLYNLDEDETQGAIAINLLPLVSQSEPGRVADEMS NSRKRVVSPICLSPCFRLLRLYTGEQNNGSLEEIDALLGCPLYLTDLEVEGKLDSLSKQEREFLCSLLFYALNWFREVVN AFCQQQDAEMKGKVLTRLQNITELQNVLGKCLAATPGYVPPPATFDSEAPEGVPSINAGGPVRKKNGKKRKSDSSKACSA ERTQADESSDGNQPDTELSELEKSAAEKETGNPLAQLQSYRPYFRELDLEVFSVLHCGLLTKSILDTEMHTEASEVVQLG PAELCFLLDDMCWKLEHVLTPGSTRRVPFLKERGNKDVGFSHLCQRSPKEVAVCVVKLLKPLCNHMENMHNYFQTVIPNQ GVVDESGLNIQEYQLMSSCYHQLLLAFRLLFAWSGFSQHENSNLLRSALQVLADRLKPGETEFLPLEELISESFQYLLNF QASIPSFQCAFILTQVLMAISEKPMTGWKREKMASLAKQFLCQSWMKPGGDREKGSHFNSALHTLLCVYLEHTDNILKAI EEISSVGVPELINSAKDGCSSTYPTLSRQTFPVFFRVMMAQLESSVKSIPAGKPSDSGEVQLEKLLKWNIAVRNFHILIN LVKVFDSRPVLSICLKYGRLFVEAFLKLAMPLLDHSFKKHRDDVQSLLKTLQLSTRQLHHMCGHSKIHQDLGLTNHVPLL KKSLEQFVYRVKAMLAFNHCQEAFWVGVLKNRDLQGEEILSQASAAPEEDSAEGSEEDTEDSAAEEPDGTDSDSGGAGR F1NP22 Fanconi anemia complementation group I Gallus gallus 0.149458297 1 Spodoptera frugiperda LEVO MAQRILQLAAEGSPERLQEALQGLTEGELGDMVTRQALRGRETAALLKGIFKGSPCSQQSGVLRRLQVYKHCVSLVESGD LHVGKVSEIIGLLMLEARQLPGHALAELATLFVEVIKRGSLSNGKSLELFSTVLTALSNSKESLAYGKGELNGEEFKKQL INTLCSSKWDPQCVIHLANMFRDIPLSGEELQFVVEKVLRMFSKLDLQEIPPLVYQLLLLSAKGSKKTVLEGIISFFNQL DKRQKEEQRVPQSADLEVATVPLDQLRHVEGTVILHIVSAINLDQDIGEELIKHLKTEQQKDPGKALCPFSVSLLLSTAV KHRLQEQIFDFLKTSITRSCKDLQILQASKFLQDLCPQQYDVTAVILEVVKNSAFGWDHVTQGLVDLGFSLMESYEPKKS FGGKAAETNLGLSKMPAQQACKLGASILLETFKVHEPIRSDILEQVLNRVLTKAASPVSHFIDLLSNIVVSAPLVLQNSS SRVTETFDNLSFLPIDTVQGLLRAVQPLLKVSMSVRDSLILVLQKAIFSRQLDARKAAVAGFLLLLRNFKILGSLTSSQC SQAIGATQVQADVHACYNSAANEAFCLEILGSLRRCLSQQADVRLMLYEGFYDVLRRNSQLASSIMETLLSQIKQYYLPQ QDLLPPLKLEGCIMAQGDQIFLQEPLAHLLCCIQHCLAWYKSTVHLCKGAEDEEEEEDVGFEQNFEEMLESVTRRMIKSE LEDFELDKSADFSPSSGVGVKNNIYAIQVMGICEVLIEYNFKIGNFSKNKFEDVLGLFTCYNKLSEILKEKAGKNKSTLG NRIARSFLSMGFVSTLLTALFRDNAQSHEESLAVLRSSTEFMRYAVSVALQKVQQLEEMGQTDGPDGQNPEKMFQNLCKI TRVLLWRYTSIPTAVEESGKKKGKSISLLCLEGLLRIFNTMQQLYAARIPQFLQALDITDGDAEEADINVTEKAAFQIRQ FQRSLVNQLSSAEDDFNSKETQLLITILSTLSKLLDPGSQQFLQFLTWTVKICKENALEDLSCCKGLLTLLFSLHVLYKS PVSLLRELAQDIHACLGDIDQDVEIESRSHFAIVNVKTAAPTVCLLVLGQADKVLEEVDWLIKRLTILGSDTSEDSTQAS NQTQALEKGVILQLGTLLTVFHELVQTALPAGSCVDSLLRSLSKTYAILTSLIKHYIQACRSTSNTVPGRLEKLVKLSGS HLTPQCYSFITYVQNIHSESLSFAEEKKKKKKEDETAVVSTVMAKVLRDTKPIPNLIFAIEQYEKFLIHLSKKSKVNLMQ YMKLSTSRDFRINASMLDSVLQEQNTEDAENEPDNNQSGTAEQPDENQEPQKKRRRKK B0I564 Polyubiquitin-C Homo sapiens 0.008576831 1 Escherichia coli LEVO MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG P0CG48 DNA (33-MER) synthetic construct 0.005898203
An idealized dsDNA of 33 bp of arbitrary sequence was placed and refined into the EM density but the following DNA sequences were used in the sample preparation by annealing oligonucleotides X1, X2, X3, X4, X5, X6: X1: GCGCACCAAGAGATACGCGGTCGAATGCCGAGTAGCCATCAGCG X2: ACCATGCAGCTACTCGGCATTCGACCGCGTATCTGGCGACTACG X3: TATCTCTTGGTGCGC X4: CGCTGATGGCTACTC X5: CGTAGTCGCCAGATA X6: GAGTAGCTGCATGGT
2 (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) DNA singleParticle particle 0.3 8.0
50 mM HEPES, 100 mM imidazole, 150 mM NaCl, 1 mM TCEP
 UltrAuFoil GOLD 300 PLASMA CLEANING ETHANE 100 277.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.8 3.5 81000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 BIOQUANTUM (6k x 4k) 70.0 1 2500000
Random model generated by stochastic gradient algorithm
 C1 3.8 FSC 0.143 CUT-OFF RELION 3.1 146245 MAXIMUM LIKELIHOOD RELION MAXIMUM LIKELIHOOD RELION RELION emd_10531.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 476.99997 476.99997 476.99997 90.0 90.0 90.0 X Y Z -0.04974713 0.10805731 0.000058346082 0.0012534399 1.06 1.06 1.06 0.0197 AUTHOR Post processed map from Relion 3S4W PDB experimental model 1UBQ PDB experimental model OTHER REAL emd_10531_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 476.99997 476.99997 476.99997 90.0 90.0 90.0 X Y Z -0.021444434 0.105293766 0.000003709677 0.00036599854 1.06 1.06 1.06 AUTHOR Focussed map for DNA region. Please use this map for DNA model fit in map. emd_10531_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 476.99997 476.99997 476.99997 90.0 90.0 90.0 X Y Z -0.016592175 0.055541914 -0.00007219136 0.0010896665 1.06 1.06 1.06 AUTHOR Refined map emd_10531_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 476.99997 476.99997 476.99997 90.0 90.0 90.0 X Y Z -0.044572268 0.0741234 -0.000072441544 0.0032467623 1.06 1.06 1.06 AUTHOR Half1 map from auto-refinement in Relion emd_10531_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 476.99997 476.99997 476.99997 90.0 90.0 90.0 X Y Z -0.049140632 0.0810616 -0.00007183393 0.0032957492 1.06 1.06 1.06 AUTHOR Half2 map from auto-refinement in Relion