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- PDB-9iju: Sertraline enhances the deubiquitinase activity of USP7 by bindin... -

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Basic information

Entry
Database: PDB / ID: 9iju
TitleSertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region
Components
  • Ubiquitin
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / ubiquitin specific protease
Function / homology
Function and homology information


regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / : / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / Formation of the ternary complex, and subsequently, the 43S complex ...regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / : / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of gene expression via chromosomal CpG island methylation / : / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / protein deubiquitination / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of gluconeogenesis / 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) / negative regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / cytosolic ribosome / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / 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 / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / VLDLR internalisation and degradation / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of signal transduction by p53 class mediator / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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. / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-SRE / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsShi, L. / Xu, Z. / Chen, X. / Xiong, B. / Zhang, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171220 China
CitationJournal: J.Med.Chem. / Year: 2025
Title: Sertraline and Astemizole Enhance the Deubiquitinase Activity of USP7 by Binding to Its Switching Loop Region.
Authors: Shi, L. / Xu, Z. / Chen, X. / Meng, Q. / Zhou, H. / Xiong, B. / Zhang, N.
History
DepositionJun 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Ubiquitin
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Ubiquitin
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,70910
Polymers198,0968
Non-polymers6122
Water1,17165
1
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)49,5242
Polymers49,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-7 kcal/mol
Surface area16270 Å2
MethodPISA
2
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8303
Polymers49,5242
Non-polymers3061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-7 kcal/mol
Surface area16510 Å2
MethodPISA
3
E: Ubiquitin carboxyl-terminal hydrolase 7
F: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)49,5242
Polymers49,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-7 kcal/mol
Surface area16260 Å2
MethodPISA
4
G: Ubiquitin carboxyl-terminal hydrolase 7
H: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8303
Polymers49,5242
Non-polymers3061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-7 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.640, 84.860, 106.780
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 41004.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein
Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62979
#3: Chemical ChemComp-SRE / (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine / Sertraline


Mass: 306.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17Cl2N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.46→20.581 Å / Num. obs: 65312 / % possible obs: 99.55 % / Redundancy: 2 % / Rmerge(I) obs: 0.04516 / Net I/σ(I): 12.84
Reflection shellResolution: 2.46→2.548 Å / Rmerge(I) obs: 0.6319 / Num. unique obs: 6466

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
xia2data scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NB8

1nb8


Resolution: 2.46→20.581 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 3263 5 %
Rwork0.218 --
obs0.2208 65263 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→20.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11852 0 40 65 11957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912123
X-RAY DIFFRACTIONf_angle_d0.9916420
X-RAY DIFFRACTIONf_dihedral_angle_d5.5457142
X-RAY DIFFRACTIONf_chiral_restr0.0541824
X-RAY DIFFRACTIONf_plane_restr0.0062166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.49670.37371200.3192709X-RAY DIFFRACTION99
2.4967-2.53560.3391130.29942732X-RAY DIFFRACTION100
2.5356-2.57710.38991040.28952704X-RAY DIFFRACTION99
2.5771-2.62150.31511460.28462646X-RAY DIFFRACTION100
2.6215-2.6690.32821480.29042706X-RAY DIFFRACTION100
2.669-2.72030.32971440.27942649X-RAY DIFFRACTION100
2.7203-2.77570.3861440.28172691X-RAY DIFFRACTION100
2.7757-2.83590.32851410.26352664X-RAY DIFFRACTION100
2.8359-2.90170.30981320.25742689X-RAY DIFFRACTION100
2.9017-2.9740.31711400.25692687X-RAY DIFFRACTION100
2.974-3.05420.31671360.25982707X-RAY DIFFRACTION100
3.0542-3.14370.3271510.26192694X-RAY DIFFRACTION100
3.1437-3.24480.32871210.24672706X-RAY DIFFRACTION100
3.2448-3.36030.31881520.24522663X-RAY DIFFRACTION100
3.3603-3.49430.28761310.23932704X-RAY DIFFRACTION100
3.4943-3.65250.29471300.23382727X-RAY DIFFRACTION100
3.6525-3.84380.29741230.22012707X-RAY DIFFRACTION100
3.8438-4.08290.23231670.19792686X-RAY DIFFRACTION100
4.0829-4.39530.23471790.17772683X-RAY DIFFRACTION100
4.3953-4.83250.22911470.16282700X-RAY DIFFRACTION100
4.8325-5.51990.2231800.18042684X-RAY DIFFRACTION100
5.5199-6.91050.2681360.21762744X-RAY DIFFRACTION100
6.9105-20.5810.23671780.18792718X-RAY DIFFRACTION98

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