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- EMDB-15284: Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitina... -

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Basic information

Entry
Database: EMDB / ID: EMD-15284
TitleCryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 without ML323 (consensus reconstruction)
Map dataGlobally sharpened map
Sample
  • Complex: USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with dsDNA
    • 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)
  • Ligand: ZINC ION
KeywordsDeubiquitinase / Complex / Enzyme-Substrate / Inhibitor / HYDROLASE
Function / homology
Function and homology information


regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / regulation of CD40 signaling pathway / double-strand break repair involved in meiotic recombination / gamete generation / monoubiquitinated protein deubiquitination / homologous chromosome pairing at meiosis / regulation of regulatory T cell differentiation / neuronal stem cell population maintenance ...regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / regulation of CD40 signaling pathway / double-strand break repair involved in meiotic recombination / gamete generation / monoubiquitinated protein deubiquitination / homologous chromosome pairing at meiosis / regulation of regulatory T cell differentiation / neuronal stem cell population maintenance / brain morphogenesis / deubiquitinase activator activity / mitotic intra-S DNA damage checkpoint signaling / DNA repair complex / skeletal system morphogenesis / skin development / seminiferous tubule development / homeostasis of number of cells / protein deubiquitination / embryonic organ development / single fertilization / interstrand cross-link repair / positive regulation of double-strand break repair via homologous recombination / regulation of DNA repair / response to UV / condensed chromosome / DNA polymerase binding / 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 / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of epithelial cell proliferation / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / ubiquitin binding / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / skeletal system development / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / response to gamma radiation / Asymmetric localization of PCP proteins / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling
Similarity search - Function
WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / 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 ...WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / 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 specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / WD domain, G-beta repeat / Ubiquitin-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / 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: 2.8 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
DepositionJun 28, 2022-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15284.png

Downloads & links

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Map

FileDownload / File: emd_15284.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobally sharpened map
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.965067 - 7.4988832
Average (Standard dev.)0.0000413695 (±0.13127278)
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_15284_msk_1.map
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Half map: #1

Fileemd_15284_half_map_1.map
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Half map: #2

Fileemd_15284_half_map_2.map
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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
Components
  • Complex: USP1(C90S)-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 with dsDNA
    • 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)
  • Ligand: ZINC ION

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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
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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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 / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fanconi anemia group I protein

MacromoleculeName: Fanconi anemia group I protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150.459125 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHMDQ KILSLAAEKT ADKLQEFLQT LREGDLTNLL QNQAVKGKVA GALLRAIFKG SPCSEEAGTL RRRKIYTCCI QLVESGDLQ KEIASEIIGL LMLEAHHFPG PLLVELANEF ISAVREGSLV NGKSLELLPI ILTALATKKE NLAYGKGVLS G EECKKQLI ...String:
MHHHHHHMDQ KILSLAAEKT ADKLQEFLQT LREGDLTNLL QNQAVKGKVA GALLRAIFKG SPCSEEAGTL RRRKIYTCCI QLVESGDLQ KEIASEIIGL LMLEAHHFPG PLLVELANEF ISAVREGSLV NGKSLELLPI ILTALATKKE NLAYGKGVLS G EECKKQLI NTLCSGRWDQ QYVIQLTSMF KDVPLTAEEV EFVVEKALSM FSKMNLQEIP PLVYQLLVLS SKGSRKSVLE GI IAFFSAL DKQHNEEQSG DELLDVVTVP SGELRHVEGT IILHIVFAIK LDYELGRELV KHLKVGQQGD SNNNLSPFSI ALL LSVTRI QRFQDQVLDL LKTSVVKSFK DLQLLQGSKF LQNLVPHRSY VSTMILEVVK NSVHSWDHVT QGLVELGFIL MDSY GPKKV LDGKTIETSP SLSRMPNQHA CKLGANILLE TFKIHEMIRQ EILEQVLNRV VTRASSPISH FLDLLSNIVM YAPLV LQSC SSKVTEAFDY LSFLPLQTVQ RLLKAVQPLL KVSMSMRDCL ILVLRKAMFA NQLDARKSAV AGFLLLLKNF KVLGSL SSS QCSQSLSVSQ VHVDVHSHYN SVANETFCLE IMDSLRRCLS QQADVRLMLY EGFYDVLRRN SQLANSVMQT LLSQLKQ FY EPKPDLLPPL KLEACILTQG DKISLQEPLD YLLCCIQHCL AWYKNTVIPL QQGEEEEEEE EAFYEDLDDI LESITNRM I KSELEDFELD KSADFSQSTS IGIKNNICAF LVMGVCEVLI EYNFSISSFS KNRFEDILSL FMCYKKLSDI LNEKAGKAK TKMANKTSDS LLSMKFVSSL LTALFRDSIQ SHQESLSVLR SSNEFMRYAV NVALQKVQQL KETGHVSGPD GQNPEKIFQN LCDITRVLL WRYTSIPTSV EESGKKEKGK SISLLCLEGL QKIFSAVQQF YQPKIQQFLR ALDVTDKEGE EREDADVSVT Q RTAFQIRQ FQRSLLNLLS SQEEDFNSKE ALLLVTVLTS LSKLLEPSSP QFVQMLSWTS KICKENSRED ALFCKSLMNL LF SLHVSYK SPVILLRDLS QDIHGHLGDI DQDVEVEKTN HFAIVNLRTA APTVCLLVLS QAEKVLEEVD WLITKLKGQV SQE TLSEEA SSQATLPNQP VEKAIIMQLG TLLTFFHELV QTALPSGSCV DTLLKDLCKM YTTLTALVRY YLQVCQSSGG IPKN MEKLV KLSGSHLTPL CYSFISYVQN KSKSLNYTGE KKEKPAAVAT AMARVLRETK PIPNLIFAIE QYEKFLIHLS KKSKV NLMQ HMKLSTSRDF KIKGNILDMV LREDGEDENE EGTASEHGGQ NKEPAKKKRK K

UniProtKB: Fanconi anemia group I protein

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 164.623828 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSMVSKRR LSKSEDKESL TEDASKTRKQ PLSKKTKKSH IANEVEENDS IFVKLLKISG IILKTGESQN QLAVDQIAFQ KKLFQTLRR HPSYPKIIEE FVSGLESYIE DEDSFRNCLL SCERLQDEEA SMGASYSKSL IKLLLGIDIL QPAIIKTLFE K LPEYFFEN ...String:
GPGSMVSKRR LSKSEDKESL TEDASKTRKQ PLSKKTKKSH IANEVEENDS IFVKLLKISG IILKTGESQN QLAVDQIAFQ KKLFQTLRR HPSYPKIIEE FVSGLESYIE DEDSFRNCLL SCERLQDEEA SMGASYSKSL IKLLLGIDIL QPAIIKTLFE K LPEYFFEN KNSDEINIPR LIVSQLKWLD RVVDGKDLTT KIMQLISIAP ENLQHDIITS LPEILGDSQH ADVGKELSDL LI ENTSLTV PILDVLSSLR LDPNFLLKVR QLVMDKLSSI RLEDLPVIIK FILHSVTAMD TLEVISELRE KLDLQHCVLP SRL QASQVK LKSKGRASSS GNQESSGQSC IILLFDVIKS AIRYEKTISE AWIKAIENTA SVSEHKVFDL VMLFIIYSTN TQTK KYIDR VLRNKIRSGC IQEQLLQSTF SVHYLVLKDM CSSILSLAQS LLHSLDQSII SFGSLLYKYA FKFFDTYCQQ EVVGA LVTH ICSGNEAEVD TALDVLLELV VLNPSAMMMN AVFVKGILDY LDNISPQQIR KLFYVLSTLA FSKQNEASSH IQDDMH LVI RKQLSSTVFK YKLIGIIGAV TMAGIMAADR SESPSLTQER ANLSDEQCTQ VTSLLQLVHS CSEQSPQASA LYYDEFA NL IQHEKLDPKA LEWVGHTICN DFQDAFVVDS CVVPEGDFPF PVKALYGLEE YDTQDGIAIN LLPLLFSQDF AKDGGPVT S QESGQKLVSP LCLAPYFRLL RLCVERQHNG NLEEIDGLLD CPIFLTDLEP GEKLESMSAK ERSFMCSLIF LTLNWFREI VNAFCQETSP EMKGKVLTRL KHIVELQIIL EKYLAVTPDY VPPLGNFDVE TLDITPHTVT AISAKIRKKG KIERKQKTDG SKTSSSDTL SEEKNSECDP TPSHRGQLNK EFTGKEEKTS LLLHNSHAFF RELDIEVFSI LHCGLVTKFI LDTEMHTEAT E VVQLGPPE LLFLLEDLSQ KLESMLTPPI ARRVPFLKNK GSRNIGFSHL QQRSAQEIVH CVFQLLTPMC NHLENIHNYF QC LAAENHG VVDGPGVKVQ EYHIMSSCYQ RLLQIFHGLF AWSGFSQPEN QNLLYSALHV LSSRLKQGEH SQPLEELLSQ SVH YLQNFH QSIPSFQCAL YLIRLLMVIL EKSTASAQNK EKIASLARQF LCRVWPSGDK EKSNISNDQL HALLCIYLEH TESI LKAIE EIAGVGVPEL INSPKDASSS TFPTLTRHTF VVFFRVMMAE LEKTVKKIEP GTAADSQQIH EEKLLYWNMA VRDFS ILIN LIKVFDSHPV LHVCLKYGRL FVEAFLKQCM PLLDFSFRKH REDVLSLLET FQLDTRLLHH LCGHSKIHQD TRLTQH VPL LKKTLELLVC RVKAMLTLNN CREAFWLGNL KNRDLQGEEI KSQNSQESTA DESEDDMSSQ ASKSKATEDG EEDEVSA GE KEQDSDESYD DSD

UniProtKB: Fanconi anemia group D2 protein

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Macromolecule #3: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.875125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPGSMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGG

UniProtKB: Polyubiquitin-C

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Macromolecule #4: Ubiquitin carboxyl-terminal hydrolase 1

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.390273 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GMPGVIPSES NGLSRGSPSK KNRLSLKFFQ KKETKRALDF TDSQENEEKA SEYRASEIDQ VVPAAQSSPI NCEKRENLLP FVGLNNLGN TSYLNSILQV LYFCPGFKSG VKHLFNIISR KKEALKDEAN QKDKGNCKED SLASYELICS LQSLIISVEQ L QASFLLNP ...String:
GMPGVIPSES NGLSRGSPSK KNRLSLKFFQ KKETKRALDF TDSQENEEKA SEYRASEIDQ VVPAAQSSPI NCEKRENLLP FVGLNNLGN TSYLNSILQV LYFCPGFKSG VKHLFNIISR KKEALKDEAN QKDKGNCKED SLASYELICS LQSLIISVEQ L QASFLLNP EKYTDELATQ PRRLLNTLRE LNPMYEGYLQ HDAQEVLQCI LGNIQETCQL LKKEEVKNVA ELPTKVEEIP HP KEEMNGI NSIEMDSMRH SEDFKEKLPK GNGKRKSDTE FGNMKKKVKL SKEHQSLEEN QRQTRSKRKA TSDTLESPPK IIP KYISEN ESPRPSQKKS RVKINWLKSA TKQPSILSKF CSLGKITTNQ GVKGQSKENE CDPEEDLGKC ESDNTTNGCG LESP GNTVT PVNVNEVKPI NKGEEQIGFE LVEKLFQGQL VLRTRCLECE SLTERREDFQ DISVPVQEDE LSKVEESSEI SPEPK TEMK TLRWAISQFA SVERIVGEDK YFCENCHHYT EAERSLLFDK MPEVITIHLK CFAASGLEFD CYGGGLSKIN TPLLTP LKL SLEEWSTKPT NDSYGLFAVV MHSGITISSG HYTASVKVTD LNSLELDKGN FVVDQMCEIG KPEPLNEEEA RGVVENY ND EEVSIRVGGN TQPSKVLNKK NVEAIGLLAA QKSKADYELY NKASNPDKVA STAFAENRNS ETSDTTGTHE SDRNKESS D QTGINISGFE NKISYVVQSL KEYEGKWLLF DDSEVKVTEE KDFLNSLSPS TSPTSTPYLL FYKKL

UniProtKB: Ubiquitin carboxyl-terminal hydrolase 1

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Macromolecule #5: WD repeat-containing protein 48

MacromoleculeName: WD repeat-containing protein 48 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.300656 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHLEV LFQGPGSMAA HHRQNTAGRR KVQVSYVIRD EVEKYNRNGV NALQLDPALN RLFTAGRDSI IRIWSVNQHK QDPYIASME HHTDWVNDIV LCCNGKTLIS ASSDTTVKVW NAHKGFCMST LRTHKDYVKA LAYAKDKELV ASAGLDRQIF L WDVNTLTA ...String:
MHHHHHHLEV LFQGPGSMAA HHRQNTAGRR KVQVSYVIRD EVEKYNRNGV NALQLDPALN RLFTAGRDSI IRIWSVNQHK QDPYIASME HHTDWVNDIV LCCNGKTLIS ASSDTTVKVW NAHKGFCMST LRTHKDYVKA LAYAKDKELV ASAGLDRQIF L WDVNTLTA LTASNNTVTT SSLSGNKDSI YSLAMNQLGT IIVSGSTEKV LRVWDPRTCA KLMKLKGHTD NVKALLLNRD GT QCLSGSS DGTIRLWSLG QQRCIATYRV HDEGVWALQV NDAFTHVYSG GRDRKIYCTD LRNPDIRVLI CEEKAPVLKM ELD RSADPP PAIWVATTKS TVNKWTLKGI HNFRASGDYD NDCTNPITPL CTQPDQVIKG GASIIQCHIL NDKRHILTKD TNNN VAYWD VLKACKVEDL GKVDFEDEIK KRFKMVYVPN WFSVDLKTGM LTITLDESDC FAAWVSAKDA GFSSPDGSDP KLNLG GLLL QALLEYWPRT HVNPMDEEEN EVNHVNGEQE NRVQKGNGYF QVPPHTPVIF GEAGGRTLFR LLCRDSGGET ESMLLN ETV PQWVIDITVD KNMPKFNKIP FYLQPHASSG AKTLKKDRLS ASDMLQVRKV MEHVYEKIIN LDNESQTTSS SNNEKPG EQ EKEEDIAVLA EEKIELLCQD QVLDPNMDLR TVKHFIWKSG GDLTLHYRQK ST

UniProtKB: WD repeat-containing protein 48

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Macromolecule #6: DNA (61-MER)

MacromoleculeName: DNA (61-MER) / type: dna / ID: 6
Details: Actual sequence: TGATCAGAGGTCATTTGAATTCATGGCTTCGAGCTTCATGTAGAGTCGACGGTGCTGGGAT
Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.17782 KDa
SequenceString:
(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)

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 1 / 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

BufferpH: 8
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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Details2x binning
Particle selectionNumber selected: 6716868
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 583484
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7ay1

chain_id: A, source_name: PDB, initial_model_type: experimental model

7ay1

chain_id: B, source_name: PDB, initial_model_type: experimental model

7ay1

chain_id: E, source_name: PDB, initial_model_type: experimental model

7zh3

source_name: PDB, initial_model_type: experimental model

6vae

chain_id: S, source_name: PDB, initial_model_type: experimental model

6vae

chain_id: T, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Overall B value: 94.9
Output model

PDB-8a9j:
Cryo-EM structure of USP1-UAF1 bound to FANCI and mono-ubiquitinated FANCD2 without ML323 (consensus reconstruction)

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