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Yorodumi- EMDB-14721: USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (focused r... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14721 | |||||||||
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Title | USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (focused refinement) | |||||||||
Map data | Locally refined, globally sharpened map | |||||||||
Sample |
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Keywords | Inhibitor / Deubiquitinase / Complex / Enzyme-Substrate / HYDROLASE | |||||||||
Function / homology | Function and homology information positive regulation of error-prone translesion synthesis / monoubiquitinated protein deubiquitination / protein deubiquitination / 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 ...positive regulation of error-prone translesion synthesis / monoubiquitinated protein deubiquitination / protein deubiquitination / 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) / 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 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / regulation of DNA repair / response to UV / cytosolic ribosome / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / skeletal system development / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.49 Å | |||||||||
Authors | Rennie ML / Walden H | |||||||||
Funding support | European Union, United Kingdom, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14721.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-14721-v30.xml emd-14721.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14721_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_14721.png | 106.9 KB | ||
Masks | emd_14721_msk_1.map emd_14721_msk_2.map emd_14721_msk_3.map | 125 MB 125 MB 125 MB | Mask map | |
Filedesc metadata | emd-14721.cif.gz | 6.7 KB | ||
Others | emd_14721_half_map_1.map.gz emd_14721_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14721 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14721 | HTTPS FTP |
-Validation report
Summary document | emd_14721_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_14721_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_14721_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_14721_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14721 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14721 | HTTPS FTP |
-Related structure data
Related structure data | 7zh4MC 7zh3C 8a9jC 8a9kC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14721.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Locally refined, globally sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14721_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_14721_msk_2.map | ||||||||||||
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Density Histograms |
-Mask #3
File | emd_14721_msk_3.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14721_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14721_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : USP1 bound to ML323 and ubiquitin conjugated to FANCD2
Entire | Name: USP1 bound to ML323 and ubiquitin conjugated to FANCD2 |
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Components |
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-Supramolecule #1: USP1 bound to ML323 and ubiquitin conjugated to FANCD2
Supramolecule | Name: USP1 bound to ML323 and ubiquitin conjugated to FANCD2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ubiquitin-60S ribosomal protein L40
Macromolecule | Name: Ubiquitin-60S ribosomal protein L40 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 8.875125 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GPGSMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGG UniProtKB: Ubiquitin-ribosomal protein eL40 fusion protein |
-Macromolecule #2: Ubiquitin carboxyl-terminal hydrolase 1
Macromolecule | Name: Ubiquitin carboxyl-terminal hydrolase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ubiquitinyl hydrolase 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 88.390273 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phe...
Macromolecule | Name: 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine type: ligand / ID: 4 / Number of copies: 1 / Formula: JDA |
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Molecular weight | Theoretical: 384.477 Da |
Chemical component information | ChemComp-JDA: |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 39 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV / Details: blotting for 3.0 seconds. |
Details | 9.3 uM USP1-UAF1, 1.8 uM FANCI-FANCD2Ub, 2.2 uM dsDNA (61 base-pairs), 18 uM ML323 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Overall B value: 80.8 | ||||||
Output model | PDB-7zh4: |