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- EMDB-14722: Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitina... -

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Basic information

Entry
Database: EMDB / ID: EMD-14722
TitleCryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction)
Map dataGlobally sharpened map
Sample
  • Complex: USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with dsDNA and ML323
    • Complex: Fanconi anemia group I protein, Fanconi anemia group D2 protein with ubiquitin conjugated to K561, Ubiquitin carboxyl-terminal hydrolase 1, WD repeat-containing protein 48
      • Protein or peptide: Fanconi anemia group I protein
      • Protein or peptide: Fanconi anemia group D2 protein
      • Protein or peptide: Polyubiquitin-C
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
      • Protein or peptide: WD repeat-containing protein 48
      • DNA: DNA (61-MER)
Function / homology
Function and homology information


positive regulation of error-prone translesion synthesis / regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / regulation of CD40 signaling pathway / double-strand break repair involved in meiotic recombination / regulation of regulatory T cell differentiation / monoubiquitinated protein deubiquitination / homologous chromosome pairing at meiosis / gamete generation / neuronal stem cell population maintenance ...positive regulation of error-prone translesion synthesis / regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / regulation of CD40 signaling pathway / double-strand break repair involved in meiotic recombination / regulation of regulatory T cell differentiation / monoubiquitinated protein deubiquitination / homologous chromosome pairing at meiosis / gamete generation / neuronal stem cell population maintenance / deubiquitinase activator activity / brain morphogenesis / mitotic intra-S DNA damage checkpoint signaling / DNA repair complex / skeletal system morphogenesis / skin development / seminiferous tubule development / positive regulation of double-strand break repair via homologous recombination / regulation of DNA-binding transcription factor activity / single fertilization / extrinsic component of mitochondrial outer membrane / protein deubiquitination / regulation of DNA repair / homeostasis of number of cells / interstrand cross-link repair / embryonic organ development / DNA polymerase binding / condensed chromosome / response to UV / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK1 recruits IKK complex / Regulation of FZD by ubiquitination / NOTCH2 Activation and Transmission of Signal to the Nucleus / Constitutive Signaling by NOTCH1 HD Domain Mutants / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / Regulation of BACH1 activity / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / p75NTR recruits signalling complexes / Regulation of innate immune responses to cytosolic DNA / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / PINK1-PRKN Mediated Mitophagy / Downregulation of ERBB2:ERBB3 signaling / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / NRIF signals cell death from the nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of protein ubiquitination / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / Downregulation of TGF-beta receptor signaling / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TP53 Regulates Transcription of DNA Repair Genes / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / Degradation of DVL / Recognition of DNA damage by PCNA-containing replication complex / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / TNFR1-induced NFkappaB signaling pathway / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Regulation of TNFR1 signaling / skeletal system development / Ubiquitin-dependent degradation of Cyclin D / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus
Similarity search - Function
Ubiquitin specific peptidase 1 / Domain of unknown function (DUF3337) / WDR48/Bun107 / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 2 domain / FANCI helical domain 1 / FANCI helical domain 2 ...Ubiquitin specific peptidase 1 / Domain of unknown function (DUF3337) / WDR48/Bun107 / FANCI solenoid 1 cap / FANCI solenoid 1 / FANCI solenoid 2 / FANCI solenoid 3 / FANCI solenoid 2 domain / FANCI helical domain 1 / FANCI helical domain 2 / Fanconi anaemia protein FancD2 nuclease / Fanconi anaemia protein FANCD2 / FANCI solenoid 4 / 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 / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin carboxyl-terminal hydrolase / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease (USP) domain profile. / Ubiquitin specific protease domain / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / G-protein beta WD-40 repeat / Trp-Asp (WD) repeats circular profile. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / Ubiquitin-like domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 1 / Polyubiquitin-C / WD repeat-containing protein 48 / Fanconi anemia group D2 protein / Fanconi anemia group I protein
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsRennie ML / Walden H
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2015-CoG-681582European Union
Medical Research Council (MRC, United Kingdom)MC_UU_12016/12 United Kingdom
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM reveals a mechanism of USP1 inhibition through a cryptic binding site.
Authors: Martin L Rennie / Connor Arkinson / Viduth K Chaugule / Helen Walden /
Abstract: Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. Ubiquitin-specific protease 1 (USP1), a nucleus-localized deubiquitinase, lies at the interface of multiple ...Repair of DNA damage is critical to genomic integrity and frequently disrupted in cancers. Ubiquitin-specific protease 1 (USP1), a nucleus-localized deubiquitinase, lies at the interface of multiple DNA repair pathways and is a promising drug target for certain cancers. Although multiple inhibitors of this enzyme, including one in phase 1 clinical trials, have been established, their binding mode is unknown. Here, we use cryo-electron microscopy to study an assembled enzyme-substrate-inhibitor complex of USP1 and the well-established inhibitor, ML323. Achieving 2.5-Å resolution, with and without ML323, we find an unusual binding mode in which the inhibitor disrupts part of the hydrophobic core of USP1. The consequent conformational changes in the secondary structure lead to subtle rearrangements in the active site that underlie the mechanism of inhibition. These structures provide a platform for structure-based drug design targeting USP1.
History
DepositionApr 5, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_14722.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobally sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å
1.06 Å/pix.
x 320 pix.
= 339.2 Å
1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.452629 - 7.8720393
Average (Standard dev.)3.0736857e-05 (±0.13011944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14722_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_14722_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_14722_half_map_2.map
Projections & Slices
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Sample components

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Entire : USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with...

EntireName: USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with dsDNA and ML323
Components
  • Complex: USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with dsDNA and ML323
    • Complex: Fanconi anemia group I protein, Fanconi anemia group D2 protein with ubiquitin conjugated to K561, Ubiquitin carboxyl-terminal hydrolase 1, WD repeat-containing protein 48
      • Protein or peptide: Fanconi anemia group I protein
      • Protein or peptide: Fanconi anemia group D2 protein
      • Protein or peptide: Polyubiquitin-C
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
      • Protein or peptide: WD repeat-containing protein 48
      • DNA: DNA (61-MER)

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Supramolecule #1: USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with...

SupramoleculeName: USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with dsDNA and ML323
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fanconi anemia group I protein, Fanconi anemia group D2 protein w...

SupramoleculeName: Fanconi anemia group I protein, Fanconi anemia group D2 protein with ubiquitin conjugated to K561, Ubiquitin carboxyl-terminal hydrolase 1, WD repeat-containing protein 48
type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Fanconi anemia group I protein

MacromoleculeName: Fanconi anemia group I protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHMDQ KILSLAAEKT ADKLQEFLQT LREGDLTNLL QNQAVKGKVA GALLRAIFKG SPCSEEAGTL RRRKIYTCCI QLVESGDLQK EIASEIIGLL MLEAHHFPGP LLVELANEFI SAVREGSLVN GKSLELLPII LTALATKKEN LAYGKGVLSG EECKKQLINT ...String:
MHHHHHHMDQ KILSLAAEKT ADKLQEFLQT LREGDLTNLL QNQAVKGKVA GALLRAIFKG SPCSEEAGTL RRRKIYTCCI QLVESGDLQK EIASEIIGLL MLEAHHFPGP LLVELANEFI SAVREGSLVN GKSLELLPII LTALATKKEN LAYGKGVLSG EECKKQLINT LCSGRWDQQY VIQLTSMFKD VPLTAEEVEF VVEKALSMFS KMNLQEIPPL VYQLLVLSSK GSRKSVLEGI IAFFSALDKQ HNEEQSGDEL LDVVTVPSGE LRHVEGTIIL HIVFAIKLDY ELGRELVKHL KVGQQGDSNN NLSPFSIALL LSVTRIQRFQ DQVLDLLKTS VVKSFKDLQL LQGSKFLQNL VPHRSYVSTM ILEVVKNSVH SWDHVTQGLV ELGFILMDSY GPKKVLDGKT IETSPSLSRM PNQHACKLGA NILLETFKIH EMIRQEILEQ VLNRVVTRAS SPISHFLDLL SNIVMYAPLV LQSCSSKVTE AFDYLSFLPL QTVQRLLKAV QPLLKVSMSM RDCLILVLRK AMFANQLDAR KSAVAGFLLL LKNFKVLGSL SSSQCSQSLS VSQVHVDVHS HYNSVANETF CLEIMDSLRR CLSQQADVRL MLYEGFYDVL RRNSQLANSV MQTLLSQLKQ FYEPKPDLLP PLKLEACILT QGDKISLQEP LDYLLCCIQH CLAWYKNTVI PLQQGEEEEE EEEAFYEDLD DILESITNRM IKSELEDFEL DKSADFSQST SIGIKNNICA FLVMGVCEVL IEYNFSISSF SKNRFEDILS LFMCYKKLSD ILNEKAGKAK TKMANKTSDS LLSMKFVSSL LTALFRDSIQ SHQESLSVLR SSNEFMRYAV NVALQKVQQL KETGHVSGPD GQNPEKIFQN LCDITRVLLW RYTSIPTSVE ESGKKEKGKS ISLLCLEGLQ KIFSAVQQFY QPKIQQFLRA LDVTDKEGEE REDADVSVTQ RTAFQIRQFQ RSLLNLLSSQ EEDFNSKEAL LLVTVLTSLS KLLEPSSPQF VQMLSWTSKI CKENSREDAL FCKSLMNLLF SLHVSYKSPV ILLRDLSQDI HGHLGDIDQD VEVEKTNHFA IVNLRTAAPT VCLLVLSQAE KVLEEVDWLI TKLKGQVSQE TLSEEASSQA TLPNQPVEKA IIMQLGTLLT FFHELVQTAL PSGSCVDTLL KDLCKMYTTL TALVRYYLQV CQSSGGIPKN MEKLVKLSGS HLTPLCYSFI SYVQNKSKSL NYTGEKKEKP AAVATAMARV LRETKPIPNL IFAIEQYEKF LIHLSKKSKV NLMQHMKLST SRDFKIKGNI LDMVLREDGE DENEEGTASE HGGQNKEPAK KKRKK

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Macromolecule #2: Fanconi anemia group D2 protein

MacromoleculeName: Fanconi anemia group D2 protein / type: protein_or_peptide / ID: 2 / Details: Ubiquitin conjugated to K561 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSMVSKRR LSKSEDKESL TEDASKTRKQ PLSKKTKKSH IANEVEENDS IFVKLLKISG IILKTGESQN QLAVDQIAFQ KKLFQTLRRH PSYPKIIEEF VSGLESYIED EDSFRNCLLS CERLQDEEAS MGASYSKSLI KLLLGIDILQ PAIIKTLFEK LPEYFFENKN ...String:
GPGSMVSKRR LSKSEDKESL TEDASKTRKQ PLSKKTKKSH IANEVEENDS IFVKLLKISG IILKTGESQN QLAVDQIAFQ KKLFQTLRRH PSYPKIIEEF VSGLESYIED EDSFRNCLLS CERLQDEEAS MGASYSKSLI KLLLGIDILQ PAIIKTLFEK LPEYFFENKN SDEINIPRLI VSQLKWLDRV VDGKDLTTKI MQLISIAPEN LQHDIITSLP EILGDSQHAD VGKELSDLLI ENTSLTVPIL DVLSSLRLDP NFLLKVRQLV MDKLSSIRLE DLPVIIKFIL HSVTAMDTLE VISELREKLD LQHCVLPSRL QASQVKLKSK GRASSSGNQE SSGQSCIILL FDVIKSAIRY EKTISEAWIK AIENTASVSE HKVFDLVMLF IIYSTNTQTK KYIDRVLRNK IRSGCIQEQL LQSTFSVHYL VLKDMCSSIL SLAQSLLHSL DQSIISFGSL LYKYAFKFFD TYCQQEVVGA LVTHICSGNE AEVDTALDVL LELVVLNPSA MMMNAVFVKG ILDYLDNISP QQIRKLFYVL STLAFSKQNE ASSHIQDDMH LVIRKQLSST VFKYKLIGII GAVTMAGIMA ADRSESPSLT QERANLSDEQ CTQVTSLLQL VHSCSEQSPQ ASALYYDEFA NLIQHEKLDP KALEWVGHTI CNDFQDAFVV DSCVVPEGDF PFPVKALYGL EEYDTQDGIA INLLPLLFSQ DFAKDGGPVT SQESGQKLVS PLCLAPYFRL LRLCVERQHN GNLEEIDGLL DCPIFLTDLE PGEKLESMSA KERSFMCSLI FLTLNWFREI VNAFCQETSP EMKGKVLTRL KHIVELQIIL EKYLAVTPDY VPPLGNFDVE TLDITPHTVT AISAKIRKKG KIERKQKTDG SKTSSSDTLS EEKNSECDPT PSHRGQLNKE FTGKEEKTSL LLHNSHAFFR ELDIEVFSIL HCGLVTKFIL DTEMHTEATE VVQLGPPELL FLLEDLSQKL ESMLTPPIAR RVPFLKNKGS RNIGFSHLQQ RSAQEIVHCV FQLLTPMCNH LENIHNYFQC LAAENHGVVD GPGVKVQEYH IMSSCYQRLL QIFHGLFAWS GFSQPENQNL LYSALHVLSS RLKQGEHSQP LEELLSQSVH YLQNFHQSIP SFQCALYLIR LLMVILEKST ASAQNKEKIA SLARQFLCRV WPSGDKEKSN ISNDQLHALL CIYLEHTESI LKAIEEIAGV GVPELINSPK DASSSTFPTL TRHTFVVFFR VMMAELEKTV KKIEPGTAAD SQQIHEEKLL YWNMAVRDFS ILINLIKVFD SHPVLHVCLK YGRLFVEAFL KQCMPLLDFS FRKHREDVLS LLETFQLDTR LLHHLCGHSK IHQDTRLTQH VPLLKKTLEL LVCRVKAMLT LNNCREAFWL GNLKNRDLQG EEIKSQNSQE STADESEDDM SSQASKSKAT EDGEEDEVSA GEKEQDSDES YDDSD

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Macromolecule #3: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGSMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGG

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Macromolecule #4: Ubiquitin carboxyl-terminal hydrolase 1

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GMPGVIPSES NGLSRGSPSK KNRLSLKFFQ KKETKRALDF TDSQENEEKA SEYRASEIDQ VVPAAQSSPI NCEKRENLLP FVGLNNLGNT SYLNSILQVL YFCPGFKSGV KHLFNIISRK KEALKDEANQ KDKGNCKEDS LASYELICSL QSLIISVEQL QASFLLNPEK ...String:
GMPGVIPSES NGLSRGSPSK KNRLSLKFFQ KKETKRALDF TDSQENEEKA SEYRASEIDQ VVPAAQSSPI NCEKRENLLP FVGLNNLGNT SYLNSILQVL YFCPGFKSGV KHLFNIISRK KEALKDEANQ KDKGNCKEDS LASYELICSL QSLIISVEQL QASFLLNPEK YTDELATQPR RLLNTLRELN PMYEGYLQHD AQEVLQCILG NIQETCQLLK KEEVKNVAEL PTKVEEIPHP KEEMNGINSI EMDSMRHSED FKEKLPKGNG KRKSDTEFGN MKKKVKLSKE HQSLEENQRQ TRSKRKATSD TLESPPKIIP KYISENESPR PSQKKSRVKI NWLKSATKQP SILSKFCSLG KITTNQGVKG QSKENECDPE EDLGKCESDN TTNGCGLESP GNTVTPVNVN EVKPINKGEE QIGFELVEKL FQGQLVLRTR CLECESLTER REDFQDISVP VQEDELSKVE ESSEISPEPK TEMKTLRWAI SQFASVERIV GEDKYFCENC HHYTEAERSL LFDKMPEVIT IHLKCFAASG LEFDCYGGGL SKINTPLLTP LKLSLEEWST KPTNDSYGLF AVVMHSGITI SSGHYTASVK VTDLNSLELD KGNFVVDQMC EIGKPEPLNE EEARGVVENY NDEEVSIRVG GNTQPSKVLN KKNVEAIGLL GGQKSKADYE LYNKASNPDK VASTAFAENR NSETSDTTGT HESDRNKESS DQTGINISGF ENKISYVVQS LKEYEGKWLL FDDSEVKVTE EKDFLNSLSP STSPTSTPYL LFYKKL

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Macromolecule #5: WD repeat-containing protein 48

MacromoleculeName: WD repeat-containing protein 48 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHLEV LFQGPGSMAA HHRQNTAGRR KVQVSYVIRD EVEKYNRNGV NALQLDPALN RLFTAGRDSI IRIWSVNQHK QDPYIASMEH HTDWVNDIVL CCNGKTLISA SSDTTVKVWN AHKGFCMSTL RTHKDYVKAL AYAKDKELVA SAGLDRQIFL WDVNTLTALT ...String:
MHHHHHHLEV LFQGPGSMAA HHRQNTAGRR KVQVSYVIRD EVEKYNRNGV NALQLDPALN RLFTAGRDSI IRIWSVNQHK QDPYIASMEH HTDWVNDIVL CCNGKTLISA SSDTTVKVWN AHKGFCMSTL RTHKDYVKAL AYAKDKELVA SAGLDRQIFL WDVNTLTALT ASNNTVTTSS LSGNKDSIYS LAMNQLGTII VSGSTEKVLR VWDPRTCAKL MKLKGHTDNV KALLLNRDGT QCLSGSSDGT IRLWSLGQQR CIATYRVHDE GVWALQVNDA FTHVYSGGRD RKIYCTDLRN PDIRVLICEE KAPVLKMELD RSADPPPAIW VATTKSTVNK WTLKGIHNFR ASGDYDNDCT NPITPLCTQP DQVIKGGASI IQCHILNDKR HILTKDTNNN VAYWDVLKAC KVEDLGKVDF EDEIKKRFKM VYVPNWFSVD LKTGMLTITL DESDCFAAWV SAKDAGFSSP DGSDPKLNLG GLLLQALLEY WPRTHVNPMD EEENEVNHVN GEQENRVQKG NGYFQVPPHT PVIFGEAGGR TLFRLLCRDS GGETESMLLN ETVPQWVIDI TVDKNMPKFN KIPFYLQPHA SSGAKTLKKD RLSASDMLQV RKVMEHVYEK IINLDNESQT TSSSNNEKPG EQEKEEDIAV LAEEKIELLC QDQVLDPNMD LRTVKHFIWK SGGDLTLHYR QKST

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Macromolecule #6: DNA (61-MER)

MacromoleculeName: DNA (61-MER) / type: dna / ID: 6 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
TGATCAGAGG TCATTTGAAT TCATGGCTTC GAGCTTCATG TAGAGTCGAC GGTGCTGGGA T

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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: 8
GridModel: UltrAuFoil R1.2/1.3 / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Details: blotted for 3.0 secs before plunging.
Details9.3 uM USP1-UAF1, 1.8 uM FANCI-FANCD2Ub, 2.2 uM dsDNA (61 base-pairs), 18 uM ML323

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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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6716868
CTF correctionSoftware - Name: cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 570816
Details2x binning
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementOverall B value: 95.3
Output model

PDB-8a9k:
Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with ML323 (consensus reconstruction)

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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