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- PDB-6jlq: Crystal structure of human USP46-WDR48-WDR20 complex -

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Basic information

Entry
Database: PDB / ID: 6jlq
TitleCrystal structure of human USP46-WDR48-WDR20 complex
Components
  • (WD repeat-containing protein ...) x 2
  • Ubiquitin carboxyl-terminal hydrolase 46
KeywordsHYDROLASE / Deubiquitinase / DUB / USP46
Function / homology
Function and homology information


regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / adult feeding behavior / righting reflex / behavioral response to ethanol / deubiquitinase activator activity / skeletal system morphogenesis / skin development / regulation of synaptic transmission, GABAergic / positive regulation of double-strand break repair via homologous recombination ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / adult feeding behavior / righting reflex / behavioral response to ethanol / deubiquitinase activator activity / skeletal system morphogenesis / skin development / regulation of synaptic transmission, GABAergic / positive regulation of double-strand break repair via homologous recombination / seminiferous tubule development / protein deubiquitination / single fertilization / homeostasis of number of cells / behavioral fear response / embryonic organ development / ubiquitin binding / positive regulation of epithelial cell proliferation / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / double-strand break repair via homologous recombination / positive regulation of receptor signaling pathway via JAK-STAT / multicellular organism growth / late endosome / single-stranded DNA binding / double-stranded DNA binding / spermatogenesis / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / intracellular membrane-bounded organelle / DNA damage response / proteolysis / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
WDR48/Bun107 / Domain of unknown function (DUF3337) / : / 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. ...WDR48/Bun107 / Domain of unknown function (DUF3337) / : / 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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Papain-like cysteine peptidase superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / cDNA FLJ33261 fis, clone ASTRO2005902, highly similar to WD repeat protein 20 / WD repeat-containing protein 20 / Ubiquitin carboxyl-terminal hydrolase 46 / WD repeat-containing protein 48 / WD repeat-containing protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.101 Å
AuthorsZhu, H. / Zhang, T. / Ding, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
Chinese Academy of Sciences China
CitationJournal: Cell Discov / Year: 2019
Title: Structural insights into the activation of USP46 by WDR48 and WDR20.
Authors: Zhu, H. / Zhang, T. / Wang, F. / Yang, J. / Ding, J.
History
DepositionMar 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 46
B: WD repeat-containing protein 48
C: WD repeat-containing protein 20,highly similar to WD repeat protein 20,WD repeat-containing protein 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,45213
Polymers159,5543
Non-polymers89710
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-2 kcal/mol
Surface area50500 Å2
Unit cell
Length a, b, c (Å)217.230, 217.230, 223.933
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ubiquitin carboxyl-terminal hydrolase 46 / Deubiquitinating enzyme 46 / Ubiquitin thioesterase 46 / Ubiquitin-specific-processing protease 46


Mass: 41262.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP46 / Production host: Escherichia coli (E. coli) / References: UniProt: P62068, ubiquitinyl hydrolase 1

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WD repeat-containing protein ... , 2 types, 2 molecules BC

#2: Protein WD repeat-containing protein 48


Mass: 69730.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TAF3
#3: Protein WD repeat-containing protein 20,highly similar to WD repeat protein 20,WD repeat-containing protein 20 / Protein DMR


Mass: 48560.879 Da / Num. of mol.: 1
Fragment: UNP residues 1-318,UNP residues 106-137,UNP residues 535-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Bos mutus (wild yak)
Gene: WDR20, M91_05678 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TBZ3, UniProt: B3KQX8, UniProt: L8I535

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Non-polymers , 3 types, 10 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 4.78 Å3/Da / Density % sol: 74.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 1.0M Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 56304 / % possible obs: 99 % / Redundancy: 11 % / Biso Wilson estimate: 88.06 Å2 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.041 / Rrim(I) all: 0.148 / Χ2: 2.519 / Net I/σ(I): 9.9 / Num. measured all: 616763
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.2111.11.855800.5190.5091.8792.09399.9
3.21-3.3411.11.13955660.7530.3211.1892.1599.9
3.34-3.4911.20.65455730.9050.1840.6832.19499.8
3.49-3.6811.10.41456070.9530.1170.4322.25499.7
3.68-3.9111.10.28255930.9780.080.2952.2999.4
3.91-4.2111.10.16656030.9910.0470.1742.42399.3
4.21-4.63110.10556180.9950.030.112.57199
4.63-5.3110.08556410.9960.0250.0892.98498.7
5.3-6.6710.40.09156680.9960.0270.0953.32998.3
6.67-5010.30.04758550.9990.0140.052.96796.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K1C

5k1c


Resolution: 3.101→43.986 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 2823 5.02 %RANDOM
Rwork0.2467 ---
obs0.2479 56224 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.11 Å2 / Biso mean: 95.0071 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.101→43.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9273 0 54 0 9327
Biso mean--93.65 --
Num. residues----1205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029518
X-RAY DIFFRACTIONf_angle_d0.46612937
X-RAY DIFFRACTIONf_chiral_restr0.0421483
X-RAY DIFFRACTIONf_plane_restr0.0041651
X-RAY DIFFRACTIONf_dihedral_angle_d11.6585603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1006-3.15410.44461340.405626462780100
3.1541-3.21140.38951420.376826472789100
3.2114-3.27320.42621370.355826192756100
3.2732-3.340.31731490.314226562805100
3.34-3.41260.33541470.308726302777100
3.4126-3.49190.30921380.302226532791100
3.4919-3.57920.28681290.283626642793100
3.5792-3.67590.28481610.273826502811100
3.6759-3.7840.32081330.27332644277799
3.784-3.90610.3081550.28182656281199
3.9061-4.04560.25431330.26392679281299
4.0456-4.20750.25321300.24192657278799
4.2075-4.39880.26641330.23332690282399
4.3988-4.63050.23411470.21842642278999
4.6305-4.92020.23621490.20292670281999
4.9202-5.29950.25671370.20692684282198
5.2995-5.83180.24431610.23352658281999
5.8318-6.67310.27861330.2372703283698
6.6731-8.39780.26691250.2272738286397
8.3978-43.99050.23331500.21242815296595

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