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- EMDB-46895: Cryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by... -

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Basic information

Entry
Database: EMDB / ID: EMD-46895
TitleCryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by KSQ-4279
Map data
Sample
  • Complex: Ternary complex of USP1-UAF1-Ubiquitin
    • Protein or peptide: WD repeat-containing protein 48
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
  • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
  • Ligand: 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine
  • Ligand: 3-(methanesulfonyl)propan-1-amine
KeywordsProtease / Thiol-protease / DNA-repair / 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 / monoubiquitinated protein deubiquitination / seminiferous tubule development / deubiquitinase activator activity / skeletal system morphogenesis / skin development / homeostasis of number of cells / protein deubiquitination ...regulation of protein monoubiquitination / positive regulation of error-prone translesion synthesis / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / monoubiquitinated protein deubiquitination / seminiferous tubule development / deubiquitinase activator activity / skeletal system morphogenesis / skin development / homeostasis of number of cells / protein deubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / embryonic organ development / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / single fertilization / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / 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 / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / regulation of DNA repair / positive regulation of double-strand break repair via homologous recombination / response to UV / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / TICAM1, RIP1-mediated IKK complex recruitment / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Fanconi Anemia Pathway / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR2 signaling / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Peroxisomal protein import / Negative regulation of FGFR4 signaling / Stabilization of p53 / Degradation of DVL / Negative regulation of FGFR1 signaling / EGFR downregulation
Similarity search - Function
WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / : / 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 ...WDR48/Bun107 / Ubiquitin specific peptidase 1 / : / Domain of unknown function (DUF3337) / : / 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 domain / Ubiquitin conserved site / 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
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGriffith JP / Wylie AA / Ali JA
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the USP1-UAF1-Ubiquitin complex inhibited by KSQ-4279
Authors: Griffith JP / Wylie AA / Ali JA
History
DepositionSep 4, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46895.png

Downloads & links

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Map

FileDownload / File: emd_46895.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 288 pix.
= 235.872 Å		0.82 Å/pix.
x 288 pix.
= 235.872 Å		0.82 Å/pix.
x 288 pix.
= 235.872 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.027116898 - 1.6004392
Average (Standard dev.)0.0011269683 (±0.023051638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 235.87201 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46895_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Half map: half map (A)

Fileemd_46895_half_map_1.map
Annotationhalf map (A)
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half map (B)

Fileemd_46895_half_map_2.map
Annotationhalf map (B)
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Ternary complex of USP1-UAF1-Ubiquitin

EntireName: Ternary complex of USP1-UAF1-Ubiquitin
Components
  • Complex: Ternary complex of USP1-UAF1-Ubiquitin
    • Protein or peptide: WD repeat-containing protein 48
    • Protein or peptide: Ubiquitin carboxyl-terminal hydrolase 1
  • Protein or peptide: Ubiquitin
  • Ligand: ZINC ION
  • Ligand: 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine
  • Ligand: 3-(methanesulfonyl)propan-1-amine

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Supramolecule #1: Ternary complex of USP1-UAF1-Ubiquitin

SupramoleculeName: Ternary complex of USP1-UAF1-Ubiquitin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: WD repeat-containing protein 48

MacromoleculeName: WD repeat-containing protein 48 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.312398 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAHHRQNTA GRRKVQVSYV IRDEVEKYNR NGVNALQLDP ALNRLFTAGR DSIIRIWSVN QHKQDPYIAS MEHHTDWVND IVLCCNGKT LISASSDTTV KVWNAHKGFC MSTLRTHKDY VKALAYAKDK ELVASAGLDR QIFLWDVNTL TALTASNNTV T TSSLSGNK ...String:
MAAHHRQNTA GRRKVQVSYV IRDEVEKYNR NGVNALQLDP ALNRLFTAGR DSIIRIWSVN QHKQDPYIAS MEHHTDWVND IVLCCNGKT LISASSDTTV KVWNAHKGFC MSTLRTHKDY VKALAYAKDK ELVASAGLDR QIFLWDVNTL TALTASNNTV T TSSLSGNK DSIYSLAMNQ LGTIIVSGST EKVLRVWDPR TCAKLMKLKG HTDNVKALLL NRDGTQCLSG SSDGTIRLWS LG QQRCIAT YRVHDEGVWA LQVNDAFTHV YSGGRDRKIY CTDLRNPDIR VLICEEKAPV LKMELDRSAD PPPAIWVATT KST VNKWTL KGIHNFRASG DYDNDCTNPI TPLCTQPDQV IKGGASIIQC HILNDKRHIL TKDTNNNVAY WDVLKACKVE DLGK VDFED EIKKRFKMVY VPNWFSVDLK TGMLTITLDE SDCFAAWVSA KDAGFSSPDG SDPKLNLGGL LLQALLEYWP RTHVN PMDE EENEVNHVNG EQENRVQKGN GYFQVPPHTP VIFGEAGGRT LFRLLCRDSG GETESMLLNE TVPQWVIDIT VDKNMP KFN KIPFYLQPHA SSGAKTLKKD RLSASDMLQV RKVMEHVYEK IINLDNESQT TSSSNNEKPG EQEKEEDIAV LAEEKIE LL CQDQVLDPNM DLRTVKHFIW KSGGDLTLHY RQKST

UniProtKB: WD repeat-containing protein 48

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Macromolecule #2: Ubiquitin carboxyl-terminal hydrolase 1

MacromoleculeName: Ubiquitin carboxyl-terminal hydrolase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.321242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPGVIPSESN GLSRGSPSKK NRLSLKFFQK KETKRALDFT DSQENEEKAS EYRASEIDQV VPAAQSSPIN CEKRENLLPF VGLNNLGNT CYLNSILQVL YFCPGFKSGV KHLFNIISRK KEALKDEANQ KDKGNCKEDS LASYELICSL QSLIISVEQL Q ASFLLNPE ...String:
MPGVIPSESN GLSRGSPSKK NRLSLKFFQK KETKRALDFT DSQENEEKAS EYRASEIDQV VPAAQSSPIN CEKRENLLPF VGLNNLGNT CYLNSILQVL YFCPGFKSGV KHLFNIISRK KEALKDEANQ KDKGNCKEDS LASYELICSL QSLIISVEQL Q ASFLLNPE KYTDELATQP RRLLNTLREL NPMYEGYLQH DAQEVLQCIL GNIQETCQLL KKEEVKNVAE LPTKVEEIPH PK EEMNGIN SIEMDSMRHS EDFKEKLPKG NGKRKSDTEF GNMKKKVKLS KEHQSLEENQ RQTRSKRKAT SDTLESPPKI IPK YISENE SPRPSQKKSR VKINWLKSAT KQPSILSKFC SLGKITTNQG VKGQSKENEC DPEEDLGKCE SDNTTNGCGL ESPG NTVTP VNVNEVKPIN KGEEQIGFEL VEKLFQGQLV LRTRCLECES LTERREDFQD ISVPVQEDEL SKVEESSEIS PEPKT EMKT LRWAISQFAS VERIVGEDKY FCENCHHYTE AERSLLFDKM PEVITIHLKC FAASGLEFDC YGGGLSKINT PLLTPL KLS LEEWSTKPTN DSYGLFAVVM HSGITISSGH YTASVKVTDL NSLELDKGNF VVDQMCEIGK PEPLNEEEAR GVVENYN DE EVSIRVGGNT QPSKVLNKKN VEAIGLLGGQ KSKADYELYN KASNPDKVAS TAFAENRNSE TSDTTGTHES DRNKESSD Q TGINISGFEN KISYVVQSLK EYEGKWLLFD DSEVKVTEEK DFLNSLSPST SPTSTPYLLF YKKL

UniProtKB: Ubiquitin carboxyl-terminal hydrolase 1

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Macromolecule #3: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.519778 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRG

UniProtKB: Polyubiquitin-C

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4...

MacromoleculeName: 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1IB8
Molecular weightTheoretical: 534.536 Da

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Macromolecule #6: 3-(methanesulfonyl)propan-1-amine

MacromoleculeName: 3-(methanesulfonyl)propan-1-amine / type: ligand / ID: 6 / Number of copies: 1 / Formula: A1A4Y
Molecular weightTheoretical: 137.201 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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ay2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 233037
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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