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- PDB-5l8e: Structure of UAF1 -

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Basic information

Entry
Database: PDB / ID: 5l8e
TitleStructure of UAF1
Components
  • Unknown
  • WD repeat-containing protein 48
KeywordsSTRUCTURAL PROTEIN / WDR48 Activates USP1/12/46 B propellar
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 / seminiferous tubule development / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization / embryonic organ development ...regulation of protein monoubiquitination / Signaling by cytosolic PDGFRA and PDGFRB fusion proteins / deubiquitinase activator activity / skeletal system morphogenesis / skin development / seminiferous tubule development / positive regulation of double-strand break repair via homologous recombination / homeostasis of number of cells / single fertilization / embryonic organ development / ubiquitin binding / positive regulation of epithelial cell proliferation / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / 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 / spermatogenesis / double-stranded DNA binding / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...WDR48/Bun107 / Domain of unknown function (DUF3337) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
WD repeat-containing protein 48
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDharadhar, S. / Sixma, T.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
KWFNKI-2014-6858 Netherlands
KWFNKI-2008-4014 Netherlands
European Research Council249997 Netherlands
CitationJournal: J.Struct.Biol. / Year: 2016
Title: A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme.
Authors: Dharadhar, S. / Clerici, M. / van Dijk, W.J. / Fish, A. / Sixma, T.K.
History
DepositionJun 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,12317
Polymers130,8333
Non-polymers1,28914
Water5,585310
1
A: WD repeat-containing protein 48
C: Unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2839
Polymers65,6382
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WD repeat-containing protein 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8398
Polymers65,1951
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.303, 131.601, 148.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 65194.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR48, KIAA1449, UAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TAF3
#2: Protein/peptide Unknown


Mass: 443.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG3350, 200mM Tri-Sodium Citrate, Bis-Tris Propane Cryo -30% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91997 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91997 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 64580 / % possible obs: 99.6 % / Redundancy: 4.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.4 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYH

1vyh


Resolution: 2.3→49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.24 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22426 3201 5 %RANDOM
Rwork0.18539 ---
obs0.18731 61324 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 58.297 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å2-0 Å2
2---2.38 Å20 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8169 0 84 310 8563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198427
X-RAY DIFFRACTIONr_bond_other_d0.0020.028120
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.95111409
X-RAY DIFFRACTIONr_angle_other_deg0.849318667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42151036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23724.076368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.596151462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6131556
X-RAY DIFFRACTIONr_chiral_restr0.070.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029393
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021911
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4785.7174156
X-RAY DIFFRACTIONr_mcbond_other2.4785.7164155
X-RAY DIFFRACTIONr_mcangle_it4.1698.5545185
X-RAY DIFFRACTIONr_mcangle_other4.1698.5555186
X-RAY DIFFRACTIONr_scbond_it2.2945.9824271
X-RAY DIFFRACTIONr_scbond_other2.2935.9824272
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8168.8496224
X-RAY DIFFRACTIONr_long_range_B_refined6.25664.3559029
X-RAY DIFFRACTIONr_long_range_B_other6.25664.3619030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 226 -
Rwork0.309 4316 -
obs--96.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.96683.8591-4.45995.0801-5.83956.7291-0.1824-0.2333-0.3085-0.3233-0.2695-0.3640.33380.33350.45190.23510.1529-0.19010.2556-0.17810.285635.223210.214771.4706
200000000000000-00.0162000.016200.0162000
300000000000000-00.0162000.016200.0162000
400000000000000-00.0162000.016200.0162000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C25 - 360
2X-RAY DIFFRACTION2C12 - 24
3X-RAY DIFFRACTION2C361 - 560
4X-RAY DIFFRACTION3D25 - 360
5X-RAY DIFFRACTION4D12 - 24
6X-RAY DIFFRACTION4D361 - 560

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