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- PDB-9dtb: Crystal structure of the WDR domain of WDR91 in complex with DR3460 -

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Basic information

Entry
Database: PDB / ID: 9dtb
TitleCrystal structure of the WDR domain of WDR91 in complex with DR3460
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. / 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 DR3460
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,4703
Polymers41,0641
Non-polymers4052
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.834, 132.976, 119.620
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-A1BBW / N-[(1R)-4-cyano-2,3-dihydro-1H-inden-1-yl]-4-[(quinazolin-4-yl)amino]benzamide


Mass: 405.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H19N5O / 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.: 80 / 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: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 12.5%(w/v) PEG 4K, 20%(v/v) 1,2,6-hexanetriol 0.02 M of each Monosaccharide 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: Jul 9, 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: 27927 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.022 / Rrim(I) all: 0.062 / Χ2: 0.781 / Net I/σ(I): 11.6 / Num. measured all: 222747
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.31-2.357.90.98113740.7730.9340.3691.0490.834100
2.35-2.3980.8713770.8390.9550.3250.9290.871100
2.39-2.4480.70313650.8560.960.2620.7510.869100
2.44-2.4980.59513910.90.9730.2220.6360.885100
2.49-2.5480.5213880.9180.9780.1930.5560.903100
2.54-2.680.39813670.9440.9860.1480.4250.89100
2.6-2.6780.33313940.9580.9890.1250.3560.915100
2.67-2.748.10.26413840.9760.9940.0980.2820.907100
2.74-2.8280.21613620.9840.9960.0810.2310.874100
2.82-2.918.10.17214030.9890.9970.0640.1840.907100
2.91-3.0180.14413850.9920.9980.0540.1540.886100
3.01-3.138.10.10613750.9950.9990.040.1130.878100
3.13-3.288.10.07914010.9970.9990.0290.0840.825100
3.28-3.458.10.05813920.99810.0220.0620.763100
3.45-3.678.10.04714140.99910.0170.050.74100
3.67-3.9580.0414060.99910.0150.0430.689100
3.95-4.3580.031408110.0110.0330.5599.9
4.35-4.9880.0251416110.0090.0270.46599.9
4.98-6.277.90.02714320.99910.010.0290.499100
6.27-507.30.0231493110.0090.0250.47198

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→25.84 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 10.986 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24249 1412 5.1 %RANDOM
Rwork0.19768 ---
obs0.19993 26469 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.874 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---1.07 Å2-0 Å2
3---1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.31→25.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 1 80 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162421
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.7933616
X-RAY DIFFRACTIONr_angle_other_deg0.4291.7445561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1715342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.525514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0110404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02613
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_it2.4382.9551365
X-RAY DIFFRACTIONr_mcbond_other2.4352.9551365
X-RAY DIFFRACTIONr_mcangle_it3.7035.2851708
X-RAY DIFFRACTIONr_mcangle_other3.7035.2871709
X-RAY DIFFRACTIONr_scbond_it3.183.2261291
X-RAY DIFFRACTIONr_scbond_other3.1783.2271292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8595.8171909
X-RAY DIFFRACTIONr_long_range_B_refined7.22927.532654
X-RAY DIFFRACTIONr_long_range_B_other7.22727.492646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 99 -
Rwork0.304 1905 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: -32.2914 Å / Origin y: -21.1996 Å / Origin z: -7.6809 Å
111213212223313233
T0.1564 Å20.0048 Å20.0009 Å2-0.0209 Å20.0387 Å2--0.0833 Å2
L3.3435 °20.2311 °20.7301 °2-2.1576 °20.5929 °2--3.4045 °2
S-0.0483 Å °0.1072 Å °0.0642 Å °0.3087 Å °-0.0612 Å °-0.2257 Å °0.0447 Å °0.0629 Å °0.1095 Å °

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