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- EMDB-11934: Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2... -

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Basic information

Entry
Database: EMDB / ID: EMD-11934
TitleCryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI
Map dataGlobally sharpened map
Sample
  • Complex: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub-dsDNA
    • Complex: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub
      • Protein or peptide: Fanconi anemia group I protein
      • Protein or peptide: Fanconi anemia group D2 protein
      • Protein or peptide: Ubiquitin-60S ribosomal protein L40
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
      • Protein or peptide: WD repeat-containing protein 48
    • Complex: DNA
      • DNA: DNA (61-MER)
  • Ligand: ZINC ION
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 / regulation of regulatory T cell differentiation / monoubiquitinated protein deubiquitination / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / 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 / regulation of regulatory T cell differentiation / monoubiquitinated protein deubiquitination / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / gamete generation / neuronal stem cell population maintenance / deubiquitinase activator activity / brain morphogenesis / DNA repair complex / mitotic intra-S DNA damage checkpoint signaling / skeletal system morphogenesis / skin development / positive regulation of double-strand break repair via homologous recombination / seminiferous tubule development / protein deubiquitination / single fertilization / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / homeostasis of number of cells / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / embryonic organ development / regulation of DNA repair / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / interstrand cross-link repair / DNA polymerase binding / response to UV / condensed chromosome / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / cytosolic ribosome / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins
Similarity search - Function
Ubiquitin specific peptidase 1 / WDR48/Bun107 / 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 ...Ubiquitin specific peptidase 1 / WDR48/Bun107 / 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. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 1 / Ubiquitin-ribosomal protein eL40 fusion protein / 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: 3.7 Å
AuthorsRennie ML / Arkinson C / Walden H
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-2015-CoG-681582 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_12016/12 United Kingdom
Citation
Journal: Nat Struct Mol Biol / Year: 2021
Title: Structural basis of FANCD2 deubiquitination by USP1-UAF1.
Authors: Martin L Rennie / Connor Arkinson / Viduth K Chaugule / Rachel Toth / Helen Walden /
Abstract: Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1-UAF1 complex is the ...Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1-UAF1 complex is the monoubiquitinated FANCI-FANCD2 heterodimer, which is involved in the repair of DNA interstrand crosslinks via the Fanconi anemia pathway. Here we determine structures of human USP1-UAF1 with and without ubiquitin and bound to monoubiquitinated FANCI-FANCD2. The crystal structures of USP1-UAF1 reveal plasticity in USP1 and key differences to USP12-UAF1 and USP46-UAF1, two related proteases. A cryo-EM reconstruction of USP1-UAF1 in complex with monoubiquitinated FANCI-FANCD2 highlights a highly orchestrated deubiquitination process, with USP1-UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for the requirement of both proteins, despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1-UAF1 regulation and substrate recognition.
#1: Journal: Biorxiv / Year: 2020
Title: Structural basis of FANCD2 deubiquitination by USP1-UAF1
Authors: Rennie ML / Arkinson C / Chaugule VK / Toth R / Walden H
History
DepositionNov 10, 2020-
Header (metadata) releaseMar 24, 2021-
Map releaseMar 24, 2021-
UpdateJul 27, 2022-
Current statusJul 27, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ay1
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11934.png

Downloads & links

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Map

FileDownload / File: emd_11934.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.)
1.02 Å/pix.
x 320 pix.
= 324.8 Å		1.02 Å/pix.
x 320 pix.
= 324.8 Å		1.02 Å/pix.
x 320 pix.
= 324.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.015 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.8290775 - 1.7649769
Average (Standard dev.)-0.001652111 (±0.050598904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0151.0151.015
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z324.800324.800324.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.8291.765-0.002

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Supplemental data

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Mask #1

Fileemd_11934_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: DeepEMhancer map using the high resolution deep learning model

Fileemd_11934_additional_1.map
AnnotationDeepEMhancer map using the high resolution deep learning model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Locally filtered and sharpened map

Fileemd_11934_additional_2.map
AnnotationLocally filtered and sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_11934_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_11934_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub-dsDNA

EntireName: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub-dsDNA
Components
  • Complex: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub-dsDNA
    • Complex: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub
      • Protein or peptide: Fanconi anemia group I protein
      • Protein or peptide: Fanconi anemia group D2 protein
      • Protein or peptide: Ubiquitin-60S ribosomal protein L40
      • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
      • Protein or peptide: WD repeat-containing protein 48
    • Complex: DNA
      • DNA: DNA (61-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub-dsDNA

SupramoleculeName: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub-dsDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 490 KDa

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Supramolecule #2: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub

SupramoleculeName: Enzyme substrate complex of USP1-UAF1 and FANCI-FANCD2ub
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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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

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Macromolecule #2: Fanconi anemia group D2 protein

MacromoleculeName: Fanconi anemia group D2 protein / type: protein_or_peptide / ID: 2 / 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

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Macromolecule #3: Ubiquitin-60S ribosomal protein L40

MacromoleculeName: Ubiquitin-60S ribosomal protein L40 / 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: Spodoptera frugiperda (fall armyworm)
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 / 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

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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

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Macromolecule #6: DNA (61-MER)

MacromoleculeName: DNA (61-MER) / type: dna / ID: 6
Details: Arbitrary DNA sequence modelled due to insufficient local resolution to determine sequence register. DNA used 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

Concentration4.3 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium chlorideNaClSodium chloride
2.0 mMC4H10O2S2DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
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: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: COUNTING / Average exposure time: 14.9 sec. / Average electron dose: 65.0 e/Å2

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Image processing

Particle selectionNumber selected: 249732
CTF correctionSoftware - Name: cryoSPARC (ver. 2.13.2)
Startup modelType of model: NONE / Details: Ab initio reconstruction in cryosparc
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.13.2) / Number images used: 391552
FSC plot (resolution estimation)

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