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- PDB-8shj: Crystal structure of the WD-repeat domain of human WDR91 in compl... -

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Basic information

Entry
Database: PDB / ID: 8shj
TitleCrystal structure of the WD-repeat domain of human WDR91 in complex with MR45279
ComponentsWD repeat-containing protein 91
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / WDR91 / SGC / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium
Function / homology
Function and homology information


phosphatidylinositol 3-kinase inhibitor activity / extrinsic component of endosome membrane / phosphatidylinositol 3-kinase regulator activity / early endosome to late endosome transport / regulation of protein catabolic process / CDC42 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / late endosome membrane / early endosome membrane / endosome membrane / cytosol
Similarity search - Function
WD repeat-containing protein 91 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / 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
Chem-ZI8 / WD repeat-containing protein 91
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsAhmad, H. / Zeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Xu, J. / Feng, J.W. / Brown, P.J. / Ackloo, S. ...Ahmad, H. / Zeng, H. / Dong, A. / Li, Y. / Hutchinson, A. / Seitova, A. / Xu, J. / Feng, J.W. / Brown, P.J. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning.
Authors: Ahmad, S. / Xu, J. / Feng, J.A. / Hutchinson, A. / Zeng, H. / Ghiabi, P. / Dong, A. / Centrella, P.A. / Clark, M.A. / Guie, M.A. / Guilinger, J.P. / Keefe, A.D. / Zhang, Y. / Cerruti, T. / ...Authors: Ahmad, S. / Xu, J. / Feng, J.A. / Hutchinson, A. / Zeng, H. / Ghiabi, P. / Dong, A. / Centrella, P.A. / Clark, M.A. / Guie, M.A. / Guilinger, J.P. / Keefe, A.D. / Zhang, Y. / Cerruti, T. / Cuozzo, J.W. / von Rechenberg, M. / Bolotokova, A. / Li, Y. / Loppnau, P. / Seitova, A. / Li, Y.Y. / Santhakumar, V. / Brown, P.J. / Ackloo, S. / Halabelian, L.
History
DepositionApr 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 91
B: WD repeat-containing protein 91
C: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,6666
Polymers118,5473
Non-polymers1,1193
Water4,738263
1
A: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8892
Polymers39,5161
Non-polymers3731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8892
Polymers39,5161
Non-polymers3731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8892
Polymers39,5161
Non-polymers3731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.859, 121.374, 131.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WD repeat-containing protein 91


Mass: 39515.785 Da / Num. of mol.: 3 / Fragment: WD repeat domains / Mutation: 15-residue deletion within the WD3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR91, HSPC049 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4D1P6
#2: Chemical ChemComp-ZI8 / N-[3-(4-chlorophenyl)oxetan-3-yl]-4-[(3S)-3-hydroxypyrrolidin-1-yl]benzamide


Mass: 372.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H21ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% (w/v) PEG3350, 0.2 M KCl, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 62725 / % possible obs: 99.7 % / Redundancy: 7.4 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.039 / Rrim(I) all: 0.106 / Χ2: 0.778 / Net I/σ(I): 5.7 / Num. measured all: 463068
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.21-2.257.30.99230800.7440.9240.3911.0680.53399.5
2.25-2.297.50.86430560.8150.9480.3360.9280.53499.6
2.29-2.337.50.75631370.8770.9670.2930.8110.54299.7
2.33-2.387.50.68130470.8940.9710.2650.7320.55199.7
2.38-2.437.30.62731160.9020.9740.2470.6750.54799.7
2.43-2.496.90.53431210.9240.980.2160.5770.5699.9
2.49-2.556.60.42130520.950.9870.1750.4570.57198.7
2.55-2.627.70.38731260.9630.990.1480.4150.587100
2.62-2.77.90.31731040.9790.9950.120.3390.615100
2.7-2.787.90.25431220.9860.9960.0960.2720.64100
2.78-2.887.80.20831390.990.9980.0790.2220.678100
2.88-37.70.17231240.9920.9980.0660.1850.70799.9
3-3.147.60.1331260.9960.9990.050.1390.76899.8
3.14-3.37.40.131140.9960.9990.0390.1080.82899.6
3.3-3.517.10.07631690.9980.9990.030.0820.95899.7
3.51-3.786.60.06531060.99810.0270.071.01598.9
3.78-4.167.80.05531750.99910.0210.0591.06699.9
4.16-4.767.60.04531960.99910.0170.0481.24199.9
4.76-67.40.04132410.99910.0160.0441.196100
6-506.80.04233740.99910.0170.0461.39799.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→46.25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.225 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.196
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1224 1.95 %RANDOM
Rwork0.211 ---
obs0.212 62656 99.4 %-
Displacement parametersBiso mean: 46.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.492 Å20 Å20 Å2
2--0.2548 Å20 Å2
3----3.7468 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.21→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 78 263 7509
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017472HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1310168HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2466SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1315HARMONIC5
X-RAY DIFFRACTIONt_it7472HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion17.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion988SEMIHARMONIC5
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_contact8152SEMIHARMONIC4
LS refinement shellResolution: 2.21→2.22 Å
RfactorNum. reflection% reflection
Rfree0.3136 -1.44 %
Rwork0.2179 1236 -
obs--86.92 %
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)
12.0478-0.0292-0.17071.5253-0.21720.9445-0.1007-0.05110.1648-0.05830.1034-0.02840.11490.0851-0.0027-0.02790.0144-0.03030.0002-0.0382-0.094281.834737.536511.9616
22.1860.32710.54211.8259-0.29591.1504-0.0930.0204-0.11930.11780.1223-0.0169-0.2030.0995-0.0293-0.05760.0050.0105-0.0491-0.0445-0.125881.677922.909953.84
35.4778-0.71031.3551.1985-0.63772.540.1161-0.1216-0.6130.0971-0.00290.19290.0223-0.3714-0.1132-0.2410.0282-0.0008-0.0134-0.0147-0.190646.320520.424928.3015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|394 - A|729 }
2X-RAY DIFFRACTION2{ B|394 - B|729 }
3X-RAY DIFFRACTION3{ C|395 - C|728 }

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