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- PDB-8w3v: Crystal structure of human WDR41 -

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Basic information

Entry
Database: PDB / ID: 8w3v
TitleCrystal structure of human WDR41
ComponentsWD repeat-containing protein 41
KeywordsPROTEIN BINDING / WD40-repeat / WDR41 / SGC / Structural Genomics / PSI-Biology / Structural Genomics Consortium
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / negative regulation of immune response / negative regulation of exocytosis / regulation of autophagy / positive regulation of GTPase activity / autophagy / lysosomal membrane / cytoplasm
Similarity search - Function
WD repeat-containing protein 41 / 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
WD repeat-containing protein 41
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHutchinson, A. / Dong, A. / Li, Y. / Seitova, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: To be published
Title: Crystal structure of human WDR41
Authors: Hutchinson, A. / Dong, A. / Li, Y. / Seitova, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionFeb 22, 2024Deposition site: RCSB / Processing site: RCSB
SupersessionMar 27, 2024ID: 6WHH
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 41
B: WD repeat-containing protein 41


Theoretical massNumber of molelcules
Total (without water)84,1602
Polymers84,1602
Non-polymers00
Water70339
1
A: WD repeat-containing protein 41


Theoretical massNumber of molelcules
Total (without water)42,0801
Polymers42,0801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WD repeat-containing protein 41


Theoretical massNumber of molelcules
Total (without water)42,0801
Polymers42,0801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)229.124, 86.006, 52.620
Angle α, β, γ (deg.)90.00, 94.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein WD repeat-containing protein 41


Mass: 42079.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR41, MSTP048 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HAD4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.5 M Sodium Malonate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 49100 / % possible obs: 95.3 % / Redundancy: 4.5 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.034 / Rrim(I) all: 0.075 / Χ2: 1.211 / Net I/σ(I): 13.4 / Num. measured all: 219586
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.70.95318910.6920.9040.5211.0940.89474.6
2.24-2.284.10.76321180.7040.9090.3980.8661.10282
2.28-2.324.30.68921440.8010.9430.3530.7790.86584.5
2.32-2.374.30.66222810.8160.9480.3430.750.8789.2
2.37-2.424.40.56323970.8810.9680.2910.6380.85793.6
2.42-2.484.50.58925040.860.9610.3090.6690.86796.9
2.48-2.544.60.53425280.9080.9760.280.6060.88998.2
2.54-2.614.70.47525620.8870.9690.2530.540.88698.9
2.61-2.684.70.37525090.9350.9830.1980.4260.93598.9
2.68-2.774.60.27225980.9620.990.1450.310.94799.3
2.77-2.874.50.20825140.9680.9920.1120.2380.98299.5
2.87-2.994.50.15425300.9860.9960.0820.1761.04598.8
2.99-3.124.20.11925270.9870.9970.0660.1371.14898.1
3.12-3.294.10.08525400.9940.9980.0460.0971.24498.1
3.29-3.494.90.07225760.9970.9990.0350.081.51799.9
3.49-3.764.80.06325650.9960.9990.0310.071.74999.7
3.76-4.144.80.05325610.9970.9990.0260.0591.79399.4
4.14-4.744.50.04525680.9980.9990.0230.0511.84798.4
4.74-5.964.30.04425720.9980.9990.0230.051.74798.7
5.96-354.60.03926150.99910.0190.0431.60698.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.36 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.78 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25261 2466 5 %RANDOM
Rwork0.21449 ---
obs0.21644 46626 95.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.532 Å2
Baniso -1Baniso -2Baniso -3
1--18.21 Å2-0 Å2-0.47 Å2
2--60.56 Å20 Å2
3----42.35 Å2
Refinement stepCycle: 1 / Resolution: 2.2→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4921 0 0 39 4960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125011
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164602
X-RAY DIFFRACTIONr_angle_refined_deg0.9131.7726848
X-RAY DIFFRACTIONr_angle_other_deg0.3281.72910481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1965656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.11516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36410709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021109
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_it5.0116.7842651
X-RAY DIFFRACTIONr_mcbond_other5.0096.7842651
X-RAY DIFFRACTIONr_mcangle_it6.86812.1653298
X-RAY DIFFRACTIONr_mcangle_other6.86712.1653299
X-RAY DIFFRACTIONr_scbond_it5.5336.9722360
X-RAY DIFFRACTIONr_scbond_other5.5326.9732361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.89412.7083551
X-RAY DIFFRACTIONr_long_range_B_refined9.98264.225062
X-RAY DIFFRACTIONr_long_range_B_other9.9864.225060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.203→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 157 -
Rwork0.315 2680 -
obs--75.51 %

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