[English] 日本語
Yorodumi
- PDB-5wch: Crystal structure of the catalytic domain of human USP9X -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cilium assembly / 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 / protein localization / regulation of circadian rhythm / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more