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- PDB-8f93: WDR5 covalently modified at Y228 by (R)-2-SF -

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Basic information

Entry
Database: PDB / ID: 8f93
TitleWDR5 covalently modified at Y228 by (R)-2-SF
ComponentsWD repeat-containing protein 5
KeywordsGENE REGULATION/INHIBITOR / covalent inhibition / Y228 / sulfonyl fluoride / PPI / GENE REGULATION / GENE REGULATION-INHIBITOR complex
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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-XKN / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTaunton, J. / Craven, G.B. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat.Chem. / Year: 2023
Title: Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes.
Authors: Chen, Y. / Craven, G.B. / Kamber, R.A. / Cuesta, A. / Zhersh, S. / Moroz, Y.S. / Bassik, M.C. / Taunton, J.
History
DepositionNov 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3Nov 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,07912
Polymers69,3272
Non-polymers1,75310
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.780, 103.022, 81.014
Angle α, β, γ (deg.)90.000, 101.545, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34663.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: (R)-2-SF modified Y228 / Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61964

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Non-polymers , 5 types, 107 molecules

#2: Chemical ChemComp-XKN / 3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride


Mass: 560.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H29FN4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→32.26 Å / Num. obs: 32875 / % possible obs: 98.95 % / Redundancy: 3.3 % / Biso Wilson estimate: 45.89 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.382 Å / Rmerge(I) obs: 0.7875 / Num. unique obs: 3285 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.26 Å / SU ML: 0.3731 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.3066
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2527 1681 5.11 %
Rwork0.203 58048 -
obs0.2055 32853 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 114 97 4921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01174978
X-RAY DIFFRACTIONf_angle_d1.23556767
X-RAY DIFFRACTIONf_chiral_restr0.0659753
X-RAY DIFFRACTIONf_plane_restr0.0089833
X-RAY DIFFRACTIONf_dihedral_angle_d9.3474728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.45631400.42752549X-RAY DIFFRACTION91.68
2.34-2.370.47251480.41582677X-RAY DIFFRACTION94.77
2.37-2.420.41171400.40452702X-RAY DIFFRACTION96.27
2.42-2.460.40951590.37292722X-RAY DIFFRACTION95.71
2.46-2.510.38371450.36692643X-RAY DIFFRACTION95.35
2.51-2.560.43081480.35852761X-RAY DIFFRACTION96.17
2.56-2.610.33291440.31412642X-RAY DIFFRACTION95.51
2.61-2.670.33571320.28982740X-RAY DIFFRACTION95.32
2.67-2.740.39161580.27492607X-RAY DIFFRACTION94.37
2.74-2.810.33861300.2612668X-RAY DIFFRACTION95.11
2.81-2.90.3271680.23642702X-RAY DIFFRACTION94.91
2.9-2.990.29771390.24052584X-RAY DIFFRACTION91.59
2.99-3.10.28481280.2372629X-RAY DIFFRACTION94.1
3.1-3.220.3061190.21962722X-RAY DIFFRACTION95.21
3.22-3.370.24291340.19492661X-RAY DIFFRACTION94.01
3.37-3.550.23261350.17742621X-RAY DIFFRACTION92.92
3.55-3.770.2651530.17992555X-RAY DIFFRACTION92.2
3.77-4.060.21481270.16282577X-RAY DIFFRACTION89.83
4.06-4.460.16861330.14462410X-RAY DIFFRACTION87
4.47-5.110.16111210.13292622X-RAY DIFFRACTION92.39
5.11-6.430.20791900.15012609X-RAY DIFFRACTION93.96
6.43-32.260.16941330.14832645X-RAY DIFFRACTION93.03

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