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- PDB-5wch: Crystal structure of the catalytic domain of human USP9X -

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Basic information

Entry
Database: PDB / ID: 5wch
TitleCrystal structure of the catalytic domain of human USP9X
ComponentsProbable ubiquitin carboxyl-terminal hydrolase FAF-X
KeywordsHYDROLASE / Deubiquitinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cytosolic ciliogenesis / K11-linked deubiquitinase activity / positive regulation of TORC2 signaling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein import into peroxisome matrix, receptor recycling / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity ...cytosolic ciliogenesis / K11-linked deubiquitinase activity / positive regulation of TORC2 signaling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein import into peroxisome matrix, receptor recycling / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity / DNA alkylation repair / protein K63-linked deubiquitination / axon extension / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / RHOV GTPase cycle / protein deubiquitination / RHOU GTPase cycle / cilium assembly / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / BMP signaling pathway / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / transforming growth factor beta receptor signaling pathway / chromosome segregation / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / neuron migration / regulation of circadian rhythm / protein localization / cilium / rhythmic process / cell migration / positive regulation of protein binding / growth cone / ubiquitinyl hydrolase 1 / amyloid fibril formation / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / protein ubiquitination / Amyloid fiber formation / cell division / cysteine-type endopeptidase activity / centrosome / negative regulation of transcription by RNA polymerase II / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Domain of unknown function DUF3517 / Domain of unknown function (DUF3517) / 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 / Armadillo-type fold
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 9X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsDong, A. / Zhang, Q. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Crystal structure and activity-based labeling reveal the mechanisms for linkage-specific substrate recognition by deubiquitinase USP9X.
Authors: Paudel, P. / Zhang, Q. / Leung, C. / Greenberg, H.C. / Guo, Y. / Chern, Y.H. / Dong, A. / Li, Y. / Vedadi, M. / Zhuang, Z. / Tong, Y.
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ubiquitin carboxyl-terminal hydrolase FAF-X
B: Probable ubiquitin carboxyl-terminal hydrolase FAF-X
C: Probable ubiquitin carboxyl-terminal hydrolase FAF-X
D: Probable ubiquitin carboxyl-terminal hydrolase FAF-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,4959
Polymers194,2334
Non-polymers2625
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.372, 79.048, 131.933
Angle α, β, γ (deg.)90.000, 103.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 1633 - 1638 / Label seq-ID: 84 - 89

Dom-IDAuth asym-IDLabel asym-ID
1CC
2AA

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.036661, -0.991269, -0.126655), (-0.992919, 0.021801, 0.116778), (-0.112997, 0.130039, -0.985049)9.03865, 3.21446, 63.1707

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Components

#1: Protein
Probable ubiquitin carboxyl-terminal hydrolase FAF-X / Deubiquitinating enzyme FAF-X / Fat facets in mammals / hFAM / Fat facets protein-related / X- ...Deubiquitinating enzyme FAF-X / Fat facets in mammals / hFAM / Fat facets protein-related / X-linked / Ubiquitin thioesterase FAF-X / Ubiquitin-specific protease 9 / X chromosome / Ubiquitin-specific-processing protease FAF-X


Mass: 48558.309 Da / Num. of mol.: 4 / Fragment: residues 1551-1970
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP9X, DFFRX, FAM, USP9 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q93008, ubiquitinyl hydrolase 1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.07 Å3/Da / Density % sol: 40.57 % / Mosaicity: 1.027 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M Diammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 52761 / % possible obs: 96.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.063 / Rrim(I) all: 0.14 / Χ2: 1.106 / Net I/σ(I): 6.4 / Num. measured all: 239510
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.544.20.86326230.6390.4630.9830.75295.6
2.54-2.594.40.8210.6780.4280.930.74296.4
2.59-2.644.50.7930.6950.4090.8950.77195.1
2.64-2.694.50.6350.7490.3280.7170.76296.8
2.69-2.754.50.5790.7890.2980.6530.77294.7
2.75-2.824.50.4870.8290.2510.5490.79695.5
2.82-2.894.50.4070.8970.2090.4590.83395.5
2.89-2.964.50.3240.9180.1660.3650.85995
2.96-3.054.50.280.9390.1440.3160.9394.3
3.05-3.154.50.2250.9610.1160.2530.94694.5
3.15-3.264.50.1790.9760.0920.2021.02394.7
3.26-3.394.50.1490.9770.0770.1681.15594.4
3.39-3.554.50.1180.9850.0610.1331.21694.9
3.55-3.734.50.1060.9880.0540.1191.27595.7
3.73-3.974.50.0960.9910.050.1091.3497.6
3.97-4.274.50.0830.9920.0420.0931.42999.4
4.27-4.74.70.0770.9940.0380.0861.60399.5
4.7-5.384.90.0780.9940.0370.0871.50899.5
5.38-6.784.80.0830.9940.0390.0921.40699.4
6.78-504.80.0640.9960.0310.0711.68298.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50.01 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2491 / WRfactor Rwork: 0.199 / FOM work R set: 0.7769 / SU B: 11.478 / SU ML: 0.251 / SU R Cruickshank DPI: 0.6062 / SU Rfree: 0.3087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.599 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2607 1087 2.1 %RANDOM
Rwork0.2072 ---
obs0.2084 51658 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117 Å2 / Biso mean: 45.341 Å2 / Biso min: 21.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20.67 Å2
2---2.29 Å20 Å2
3---3.21 Å2
Refinement stepCycle: final / Resolution: 2.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 0 5 40 10761
Biso mean--31.96 35.7 -
Num. residues----1354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911013
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210079
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.94114876
X-RAY DIFFRACTIONr_angle_other_deg0.872323046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35351341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43223.752541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.814151802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7321564
X-RAY DIFFRACTIONr_chiral_restr0.0720.21557
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022738
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: C / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
15MEDIUM POSITIONAL0.020.5
36TIGHT THERMAL2.030.5
15MEDIUM THERMAL2.222
LS refinement shellResolution: 2.504→2.569 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 73 -
Rwork0.317 3622 -
all-3695 -
obs--91.66 %

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