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- PDB-5cvl: WDR48 (UAF-1), residues 2-580 -

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Basic information

Entry
Database: PDB / ID: 5cvl
TitleWDR48 (UAF-1), residues 2-580
ComponentsWD repeat-containing protein 48
KeywordsPROTEIN BINDING / WDR48 / UAF1 / WD-repeat / USP / deubiquitinase / DUB
Function / homology
Function and homology information


regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / positive regulation of double-strand break repair via homologous recombination / seminiferous tubule development / single fertilization / homeostasis of number of cells / embryonic organ development ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / positive regulation of double-strand break repair via homologous recombination / seminiferous tubule development / single fertilization / homeostasis of number of cells / 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 / lysosome / Ub-specific processing proteases / intracellular membrane-bounded organelle / DNA damage response / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
WDR48/Bun107 / Domain of unknown function (DUF3337) / 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. ...WDR48/Bun107 / Domain of unknown function (DUF3337) / 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
Similarity search - Domain/homology
: / PHOSPHATE ION / WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsHARRIS, S.F. / YIN, J.
CitationJournal: Structure / Year: 2015
Title: Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46.
Authors: Yin, J. / Schoeffler, A.J. / Wickliffe, K. / Newton, K. / Starovasnik, M.A. / Dueber, E.C. / Harris, S.F.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,72010
Polymers67,1511
Non-polymers1,5699
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.520, 139.520, 235.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

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Components

#1: Protein WD repeat-containing protein 48 / USP1-associated factor 1 / WD repeat endosomal protein / p80


Mass: 67150.906 Da / Num. of mol.: 1 / Fragment: UNP residues 2-580
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48, KIAA1449, UAF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8TAF3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#3: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 4.26 Å3/Da / Density % sol: 71.12 % / Mosaicity: 0.359 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.72 M sodium phosphate, 0.72 M potassium phosphate, 90 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.026382 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: DOUBLE CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.026382 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 44419 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 81.5 Å2 / Rmerge(I) obs: 0.123 / Χ2: 1.069 / Net I/av σ(I): 19.429 / Net I/σ(I): 7.3 / Num. measured all: 381541
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2
3-3.118.60.82744150.85
3.11-3.238.60.5744380.916
3.23-3.388.60.36544660.991
3.38-3.568.60.24644431.114
3.56-3.788.60.18344381.159
3.78-4.078.60.14344141.165
4.07-4.488.60.10744521.093
4.48-5.138.50.08844571.084
5.13-6.468.50.09644271.199
6.46-508.50.04144691.12

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-2000data scaling
BUSTER-TNT2.11.5refinement
PDB_EXTRACT3.2data extraction
DENZOdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3→49.33 Å / Cor.coef. Fo:Fc: 0.9324 / Cor.coef. Fo:Fc free: 0.8988 / SU R Cruickshank DPI: 0.455 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.475 / SU Rfree Blow DPI: 0.297 / SU Rfree Cruickshank DPI: 0.297
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1999 8.47 %RANDOM
Rwork0.1862 ---
obs0.1901 23602 99.95 %-
Displacement parametersBiso max: 175.41 Å2 / Biso mean: 69.95 Å2 / Biso min: 16.53 Å2
Baniso -1Baniso -2Baniso -3
1-6.6536 Å20 Å20 Å2
2--6.6536 Å20 Å2
3----13.3072 Å2
Refine analyzeLuzzati coordinate error obs: 0.378 Å
Refinement stepCycle: final / Resolution: 3→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 17 137 4292
Biso mean--121.02 57.89 -
Num. residues----526
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1473SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes604HARMONIC5
X-RAY DIFFRACTIONt_it4232HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion561SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4806SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4232HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5744HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion22.76
LS refinement shellResolution: 3→3.13 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3404 239 8.5 %
Rwork0.2605 2573 -
all0.2673 2812 -
obs--99.95 %

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