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- PDB-8y9a: The Crystal Structure of USP8 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8y9a
TitleThe Crystal Structure of USP8 from Biortus.
ComponentsUbiquitin carboxyl-terminal hydrolase 8
KeywordsHYDROLASE / Protease / Thiol protease / Cell cycle / Ubl conjugation pathway
Function / homology
Function and homology information


regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / protein K48-linked deubiquitination / endosome organization / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / extrinsic component of plasma membrane / protein deubiquitination ...regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / protein K48-linked deubiquitination / endosome organization / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / positive regulation of amyloid fibril formation / extrinsic component of plasma membrane / protein deubiquitination / mitotic cytokinesis / Regulation of FZD by ubiquitination / Downregulation of ERBB2:ERBB3 signaling / cellular response to dexamethasone stimulus / cellular response to nerve growth factor stimulus / regulation of protein stability / Negative regulation of MET activity / SH3 domain binding / regulation of protein localization / positive regulation of canonical Wnt signaling pathway / midbody / ubiquitinyl hydrolase 1 / Ras protein signal transduction / cysteine-type deubiquitinase activity / dendritic spine / postsynaptic density / early endosome / endosome membrane / Ub-specific processing proteases / cadherin binding / cysteine-type endopeptidase activity / glutamatergic synapse / proteolysis / nucleus / cytosol / cytoplasm
Similarity search - Function
: / USP8 WW domain / USP8 dimerisation domain / USP8 dimerisation domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. ...: / USP8 WW domain / USP8 dimerisation domain / USP8 dimerisation domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 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
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of USP8 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
History
DepositionFeb 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 8


Theoretical massNumber of molelcules
Total (without water)16,7881
Polymers16,7881
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.008, 103.008, 93.254
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-213-

HOH

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 8 / Deubiquitinating enzyme 8 / Ubiquitin isopeptidase Y / hUBPy / Ubiquitin thioesterase 8 / Ubiquitin- ...Deubiquitinating enzyme 8 / Ubiquitin isopeptidase Y / hUBPy / Ubiquitin thioesterase 8 / Ubiquitin-specific-processing protease 8


Mass: 16788.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP8, KIAA0055, UBPY / Production host: Escherichia coli (E. coli) / References: UniProt: P40818, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4.0M Na formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.23985 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 3.1→40.24 Å / Num. obs: 3507 / % possible obs: 98.7 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.6
Reflection shellResolution: 3.1→3.31 Å / Rmerge(I) obs: 0.824 / Num. unique obs: 640

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→40.24 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.892 / SU B: 18.565 / SU ML: 0.326 / Cross valid method: FREE R-VALUE / ESU R Free: 0.486
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2681 166 4.733 %
Rwork0.1979 3341 -
all0.201 --
obs-3507 97.824 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 87.712 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å21.31 Å20 Å2
2--2.62 Å20 Å2
3----8.5 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 0 29 1089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0121076
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161030
X-RAY DIFFRACTIONr_angle_refined_deg0.7491.6671438
X-RAY DIFFRACTIONr_angle_other_deg0.2721.5762420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.38158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27110230
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.7251053
X-RAY DIFFRACTIONr_chiral_restr0.0360.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
X-RAY DIFFRACTIONr_nbd_refined0.2260.2265
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.2926
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2537
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.2562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.236
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.221
X-RAY DIFFRACTIONr_nbd_other0.1510.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.29
X-RAY DIFFRACTIONr_mcbond_it3.4549.046507
X-RAY DIFFRACTIONr_mcbond_other3.429.049507
X-RAY DIFFRACTIONr_mcangle_it5.30713.543632
X-RAY DIFFRACTIONr_mcangle_other5.30713.551633
X-RAY DIFFRACTIONr_scbond_it3.3519.41569
X-RAY DIFFRACTIONr_scbond_other3.3459.406568
X-RAY DIFFRACTIONr_scangle_it5.54713.961806
X-RAY DIFFRACTIONr_scangle_other5.54313.967807
X-RAY DIFFRACTIONr_lrange_it9.399123.5391284
X-RAY DIFFRACTIONr_lrange_other9.373123.8111278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.40690.172246X-RAY DIFFRACTION99.2218
3.18-3.2670.294140.238228X-RAY DIFFRACTION98.7755
3.267-3.3610.27880.298242X-RAY DIFFRACTION99.2063
3.361-3.4640.281100.26225X-RAY DIFFRACTION98.3264
3.464-3.5760.254120.263223X-RAY DIFFRACTION99.5763
3.576-3.7010.24660.227216X-RAY DIFFRACTION99.1071
3.701-3.8390.338150.237195X-RAY DIFFRACTION98.5915
3.839-3.9950.358160.242187X-RAY DIFFRACTION97.5962
3.995-4.170.35980.222190X-RAY DIFFRACTION98.5075
4.17-4.3720.179140.191174X-RAY DIFFRACTION98.4293
4.372-4.6050.30980.173176X-RAY DIFFRACTION98.3957
4.605-4.880.24430.186169X-RAY DIFFRACTION97.1751
4.88-5.2120.395140.211142X-RAY DIFFRACTION96.8944
5.212-5.6220.308110.207146X-RAY DIFFRACTION98.125
5.622-6.1460.22630.227136X-RAY DIFFRACTION96.5278
6.146-6.8520.11350.182120X-RAY DIFFRACTION95.4198
6.852-7.8743.05710.161107X-RAY DIFFRACTION94.7368
7.874-9.5530.0940.10597X-RAY DIFFRACTION96.1905
9.553-13.1450.12430.10473X-RAY DIFFRACTION93.8272
13.145-40.240.13320.19349X-RAY DIFFRACTION91.0714

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