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- PDB-9mk7: Crystal structure of the WDR domain of WDR91 in complex with DR3634 -

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Basic information

Entry
Database: PDB / ID: 9mk7
TitleCrystal structure of the WDR domain of WDR91 in complex with DR3634
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: 2.31 Å
AuthorsZeng, H. / Ahmad, H. / Dong, A. / Seitova, A. / Owen, D. / 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 DR3634
Authors: Zeng, H. / Ahmad, H. / Dong, A. / Seitova, A. / Owen, D. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionDec 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,4753
Polymers41,0641
Non-polymers4112
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.201, 132.236, 118.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 41064.477 Da / Num. of mol.: 1 / 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-A1BLV / (1R)-1-({(6M)-2-(methylamino)-6-[3-(pyrrolidin-1-yl)phenyl]pyrimidin-4-yl}amino)-2,3-dihydro-1H-indene-4-carbonitrile


Mass: 410.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26N6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.77 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M of each alcohol,0.1M MES/imidazole pH6.5
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: Oct 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 27368 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.027 / Rrim(I) all: 0.076 / Χ2: 1.043 / Net I/σ(I): 12.5 / Num. measured all: 215906
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.31-2.3570.97113430.6940.9050.391.0491.01100
2.35-2.397.70.94313600.7360.9210.361.0111.04299.9
2.39-2.447.90.82313280.8270.9510.310.881.081100
2.44-2.497.90.76413650.8210.9490.2870.8171.093100
2.49-2.5480.59313530.880.9680.2230.6351.118100
2.54-2.680.51513390.9050.9750.1930.551.127100
2.6-2.6780.4213530.9410.9850.1580.4491.099100
2.67-2.7480.33813650.9580.9890.1260.3611.121100
2.74-2.8280.27413790.9690.9920.1030.2931.126100
2.82-2.9180.2213240.9820.9950.0820.2351.106100
2.91-3.0180.18213700.9880.9970.0680.1941.146100
3.01-3.1380.13113620.9920.9980.0490.141.127100
3.13-3.2880.09313740.9960.9990.0350.10.987100
3.28-3.458.10.06813620.9980.9990.0250.0730.938100
3.45-3.6780.05213860.99810.020.0561.037100
3.67-3.9580.04713630.99910.0180.051.025100
3.95-4.3580.03613760.99910.0130.0380.671100
4.35-4.987.90.02813990.99910.0110.030.941100
4.98-6.277.90.0291407110.0110.0311.145100
6.27-507.30.0241460110.0090.0250.92198.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→25.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.398 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23777 1376 5 %RANDOM
Rwork0.1998 ---
obs0.20171 25931 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0 Å20 Å2
2---0.57 Å2-0 Å2
3---1.26 Å2
Refinement stepCycle: 1 / Resolution: 2.31→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 1 76 2621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122627
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162390
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.7923578
X-RAY DIFFRACTIONr_angle_other_deg0.4731.7385498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4065341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.556511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71510393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
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_it2.842.8221361
X-RAY DIFFRACTIONr_mcbond_other2.8392.8221361
X-RAY DIFFRACTIONr_mcangle_it4.3725.0571703
X-RAY DIFFRACTIONr_mcangle_other4.3715.0591704
X-RAY DIFFRACTIONr_scbond_it3.5153.0691266
X-RAY DIFFRACTIONr_scbond_other3.5133.0711267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3335.5191876
X-RAY DIFFRACTIONr_long_range_B_refined7.65525.892634
X-RAY DIFFRACTIONr_long_range_B_other7.65725.852624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.315→2.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 85 -
Rwork0.317 1823 -
obs--95.98 %
Refinement TLS params.Method: refined / Origin x: -31.3823 Å / Origin y: -21.1446 Å / Origin z: -7.806 Å
111213212223313233
T0.1938 Å20.0045 Å2-0.0079 Å2-0.0138 Å20.0336 Å2--0.0903 Å2
L3.6883 °20.1505 °20.7661 °2-1.9603 °20.639 °2--3.3379 °2
S-0.0496 Å °0.0958 Å °0.1024 Å °0.2489 Å °-0.074 Å °-0.2383 Å °0.0207 Å °0.0501 Å °0.1236 Å °

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