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- PDB-6vyc: Crystal structure of WD-repeat domain of human WDR91 -

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Basic information

Entry
Database: PDB / ID: 6vyc
TitleCrystal structure of WD-repeat domain of human WDR91
ComponentsWD repeat-containing protein 91
KeywordsPROTEIN TRANSPORT / WDR91 / WD-repeat / Structural Genomics / Structural Genomics Consortium / SGC
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
WD repeat-containing protein 91
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsHalabelian, L. / Hutchinson, A. / Li, Y. / Seitova, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
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
DepositionFeb 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 1, 2024Group: Database references / Category: 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


Theoretical massNumber of molelcules
Total (without water)82,1296
Polymers82,1292
Non-polymers04
Water2,288127
1
A: WD repeat-containing protein 91


Theoretical massNumber of molelcules
Total (without water)41,0644
Polymers41,0641
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 91


Theoretical massNumber of molelcules
Total (without water)41,0642
Polymers41,0641
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.004, 84.047, 110.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 394 - 730 / Label seq-ID: 21 - 372

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% PEG20000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→46.111 Å / Num. obs: 41340 / % possible obs: 97.6 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.034 / Rrim(I) all: 0.098 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.168.30.9062708032690.8270.3310.9662.895.6
8.91-46.076.60.02742926460.9990.0110.0351.799.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OW8

3ow8


Resolution: 2.1→46.07 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 13.061 / SU ML: 0.164 / SU R Cruickshank DPI: 0.2452 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.194
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2085 5 %RANDOM
Rwork0.2212 ---
obs0.2227 39208 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.1 Å2 / Biso mean: 39.507 Å2 / Biso min: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å2-0 Å2-0 Å2
2---0.83 Å20 Å2
3---2.63 Å2
Refinement stepCycle: final / Resolution: 2.1→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 4 127 5005
Biso mean--47.34 37.33 -
Num. residues----661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174460
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.6276834
X-RAY DIFFRACTIONr_angle_other_deg1.2091.56710324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5975665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64723.024205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72815755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5131518
X-RAY DIFFRACTIONr_chiral_restr0.0520.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021024
Refine LS restraints NCS

Ens-ID: 1 / Number: 9137 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 149 -
Rwork0.282 2783 -
all-2932 -
obs--95.07 %
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)
13.14540.6499-0.61522.5152-0.5231.7852-0.02950.19850.1305-0.05830.0359-0.2385-0.0592-0.0637-0.00640.00980.0098-0.00890.0346-0.02130.078315.791931.596217.5425
21.8728-0.76130.46023.793-0.30272.17030.1001-0.1332-0.0404-0.0560.02950.50660.0448-0.2065-0.12960.0432-0.0172-0.05350.0335-0.00550.222715.285471.490519.7132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A394 - 730
2X-RAY DIFFRACTION2B394 - 730

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