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- PDB-2ayn: Structure of USP14, a proteasome-associated deubiquitinating enzyme -

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Basic information

Entry
Database: PDB / ID: 2ayn
TitleStructure of USP14, a proteasome-associated deubiquitinating enzyme
ComponentsUbiquitin carboxyl-terminal hydrolase 14
KeywordsHYDROLASE / deubiquitinating enzymes / DUB / USP14 / proteasome / enzyme mechanism
Function / homology
Function and homology information


negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of proteasomal protein catabolic process / negative regulation of ubiquitin-dependent protein catabolic process / proteasome complex ...negative regulation of ERAD pathway / deubiquitinase activity / regulation of chemotaxis / K63-linked deubiquitinase activity / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of proteasomal protein catabolic process / negative regulation of ubiquitin-dependent protein catabolic process / proteasome complex / Regulation of NF-kappa B signaling / chemical synaptic transmission / cytoplasmic vesicle / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / innate immune response / synapse / cell surface / extracellular exosome / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 14-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. / Cysteine proteinases / Cathepsin B; Chain A ...Ubiquitin carboxyl-terminal hydrolase 14-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. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsHu, M. / Li, P. / Jeffrey, P.D. / Shi, Y.
CitationJournal: Embo J. / Year: 2005
Title: Structure and mechanisms of the proteasome-associated deubiquitinating enzyme USP14.
Authors: Hu, M. / Li, P. / Song, L. / Jeffrey, P.D. / Chenova, T.A. / Wilkinson, K.D. / Cohen, R.E. / Shi, Y.
History
DepositionSep 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 14
B: Ubiquitin carboxyl-terminal hydrolase 14
C: Ubiquitin carboxyl-terminal hydrolase 14


Theoretical massNumber of molelcules
Total (without water)138,6313
Polymers138,6313
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.285, 121.582, 166.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 14 / Ubiquitin thiolesterase 14 / Ubiquitin-specific processing protease 14 / Deubiquitinating enzyme 14


Mass: 46210.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP14, TGT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54578, EC: 3.1.2.15

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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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, ammonium sulfate, PEG monomethyl ether, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1, 0.9793, 0.9795, 0.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 20, 2003
RadiationMonochromator: monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97931
30.97951
40.951
ReflectionResolution: 3.2→99 Å / Num. all: 27624 / Num. obs: 27320 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.3 Å / % possible all: 96.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 3.2→99 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.322 2645 random
Rwork0.261 --
all0.265 27624 -
obs0.262 25614 -
Refinement stepCycle: LAST / Resolution: 3.2→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8163 0 0 0 8163
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_bond_d0.011

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