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- PDB-2a9u: Structure of the N-terminal domain of Human Ubiquitin carboxyl-te... -

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Basic information

Entry
Database: PDB / ID: 2a9u
TitleStructure of the N-terminal domain of Human Ubiquitin carboxyl-terminal hydrolase 8 (USP8)
ComponentsUbiquitin carboxyl-terminal hydrolase 8
KeywordsHYDROLASE / coil-coil / Protease / SH3-binding / Thiol protease / Ubl conjugation pathway / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / endosome organization / protein K48-linked deubiquitination / protein K63-linked deubiquitination / positive regulation of amyloid fibril formation / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / extrinsic component of plasma membrane / protein deubiquitination ...regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of lysosomal protein catabolic process / endosome organization / protein K48-linked deubiquitination / protein K63-linked deubiquitination / positive regulation of amyloid fibril formation / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / 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 / positive regulation of canonical Wnt signaling pathway / regulation of protein localization / 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 / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Ubiquitin specific protease (USP) domain signature 2. ...: / USP8 WW domain / USP8 dimerisation domain / USP8 dimerisation domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, E. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C. / Edwards, E. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Amino-terminal Dimerization, NRDP1-Rhodanese Interaction, and Inhibited Catalytic Domain Conformation of the Ubiquitin-specific Protease 8 (USP8).
Authors: Avvakumov, G.V. / Walker, J.R. / Xue, S. / Finerty Jr., P.J. / Mackenzie, F. / Newman, E.M. / Dhe-Paganon, S.
History
DepositionJul 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 8
B: Ubiquitin carboxyl-terminal hydrolase 8


Theoretical massNumber of molelcules
Total (without water)34,0522
Polymers34,0522
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-22 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.682, 64.820, 151.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a homodimer.

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 8 / Ubiquitin thiolesterase 8 / Ubiquitin-specific processing protease 8 / Deubiquitinating enzyme 8 / ...Ubiquitin thiolesterase 8 / Ubiquitin-specific processing protease 8 / Deubiquitinating enzyme 8 / hUBPy / USP8


Mass: 17026.145 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP8, KIAA0055, UBPY / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40818, EC: 3.1.2.15
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.68 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 27% PEG3350, 0.2 M Li2SO4, 0.1 M bisTris, pH 5.6, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97883 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.1→33.81 Å / Num. all: 18987 / Num. obs: 18987 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3.15 / Num. unique all: 16 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→33.81 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.565 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25943 976 5.2 %RANDOM
Rwork0.20829 ---
obs0.21091 17952 90.56 %-
all-18934 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---0.89 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2186 0 0 88 2274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222218
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9962962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.65259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52724.414111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29815478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3821518
X-RAY DIFFRACTIONr_chiral_restr0.090.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021620
X-RAY DIFFRACTIONr_nbd_refined0.2230.2982
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.25
X-RAY DIFFRACTIONr_mcbond_it2.21131359
X-RAY DIFFRACTIONr_mcangle_it3.23942114
X-RAY DIFFRACTIONr_scbond_it4.8415972
X-RAY DIFFRACTIONr_scangle_it7.3897848
LS refinement shellResolution: 2.1→2.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 66 -
Rwork0.243 1125 -
obs--79.14 %

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