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- PDB-9dta: Crystal structure of the WDR domain of WDR91 in complex with DR3448 -

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Basic information

Entry
Database: PDB / ID: 9dta
TitleCrystal structure of the WDR domain of WDR91 in complex with DR3448
ComponentsWD repeat-containing protein 91
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / WDR91 / SGC / Structural Genomics / PSI-Biology / Structural Genomics Consortium
Function / homology
Function and homology information


phosphatidylinositol 3-kinase inhibitor activity / 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 / : / Armc9, CTLH-like domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / WD repeat-containing protein 91
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZeng, H. / Ahmad, H. / Dong, A. / Seitova, A. / Counago, R.M. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of the WDR domain of WDR91 in complex with DR3448
Authors: Zeng, H. / Ahmad, H. / Dong, A. / Seitova, A. / Counago, R.M. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionSep 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 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 91
B: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9804
Polymers82,1292
Non-polymers8512
Water2,486138
1
A: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4902
Polymers41,0641
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4902
Polymers41,0641
Non-polymers4251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.428, 76.316, 77.043
Angle α, β, γ (deg.)119.12, 95.90, 102.57
Int Tables number1
Space group name H-MP1

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Components

#1: Protein WD repeat-containing protein 91 / WDR91


Mass: 41064.477 Da / Num. of mol.: 2 / Fragment: UNP residues 392-747
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-A1BBV / N-(1-benzoyl-1,2,3,4-tetrahydroquinolin-6-yl)-2-(3-cyano-2-methoxyphenyl)acetamide


Mass: 425.479 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H23N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10%(w/v) PEG 8K, 20%(v/v) 1,5-pentanediol 0.02 M of each Amino-acid II 0.1 M MOPSO/bis-tris pH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 50289 / % possible obs: 95 % / Redundancy: 5 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.03 / Rrim(I) all: 0.068 / Χ2: 1.073 / Net I/σ(I): 14.8 / Num. measured all: 252710
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1440.69921790.7310.9190.3750.7961.14684.1
2.14-2.184.30.60823710.7890.9390.320.691.13788.7
2.18-2.224.60.55324260.8190.9490.2830.6231.12691.7
2.22-2.264.90.53524860.8430.9560.2680.5991.18194
2.26-2.315.10.50824950.8640.9630.2510.5671.17193.4
2.31-2.375.20.43724790.8850.9690.2130.4861.14594.9
2.37-2.425.20.39125400.9230.980.190.4351.12894.4
2.42-2.495.20.35125000.9330.9820.170.391.295.1
2.49-2.565.20.28325230.9590.990.1370.3151.16595
2.56-2.655.20.22925220.9720.9930.1110.2551.12895.7
2.65-2.745.20.17425370.9840.9960.0850.1931.08795.7
2.74-2.855.20.13525430.9890.9970.0660.151.0496
2.85-2.985.20.10925710.9930.9980.0530.1211.06296.7
2.98-3.145.20.0825490.9960.9990.0390.0891.04896.9
3.14-3.335.20.05825820.9980.9990.0280.0650.95997.2
3.33-3.595.20.04525650.99810.0220.051.03897.4
3.59-3.955.20.03725930.99910.0180.0421.14597.7
3.95-4.525.10.02926300.99910.0140.0330.96598.4
4.52-5.75.10.02625900.99910.0130.0290.84698.9
5.7-504.90.02426080.99910.0120.0270.80798

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28.05 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.198 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23279 1369 2.7 %RANDOM
Rwork0.18772 ---
obs0.1889 48873 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.488 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20.62 Å20.73 Å2
2--0.45 Å20.9 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.1→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 0 138 5184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164748
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.7937065
X-RAY DIFFRACTIONr_angle_other_deg0.4461.7410913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4295671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.716522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.910786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0650.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
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_it2.9393.2682690
X-RAY DIFFRACTIONr_mcbond_other2.9393.2682690
X-RAY DIFFRACTIONr_mcangle_it4.2295.8463359
X-RAY DIFFRACTIONr_mcangle_other4.235.8483360
X-RAY DIFFRACTIONr_scbond_it3.2563.5112504
X-RAY DIFFRACTIONr_scbond_other3.2563.5112503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7826.3643707
X-RAY DIFFRACTIONr_long_range_B_refined6.82731.15270
X-RAY DIFFRACTIONr_long_range_B_other6.81731.075250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 93 -
Rwork0.303 3065 -
obs--80.75 %
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)
14.24310.79180.62133.1273-0.17752.96380.09860.03910.18660.1796-0.1160.2731-0.0464-0.14810.01750.0117-0.00280.01750.02650.00450.043212.200529.7874-22.4378
23.8177-0.82180.37532.8021-0.2022.8238-0.1947-0.17930.10830.10330.0643-0.2793-0.0440.1850.13040.02870.0103-0.03730.05610.03190.105829.7768-2.99561.8465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A394 - 801
2X-RAY DIFFRACTION2B394 - 801

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