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- PDB-6dya: WDR5 in complex with a WIN site inhibitor -

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Basic information

Entry
Database: PDB / ID: 6dya
TitleWDR5 in complex with a WIN site inhibitor
ComponentsWD repeat-containing protein 5
KeywordsTRANSFERASE/TRANSFERASE inhibitor / WD40 repeat / epigenetics / MLL binding / WIN site inhibitor / TRANSFERASE-TRANSFERASE 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 / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / 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
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
Chem-HHM / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.56 Å
AuthorsPhan, J. / Wang, F. / Fesik, S.W.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA68485 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor085P100817 United States
CitationJournal: Cell Rep / Year: 2019
Title: Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity.
Authors: Aho, E.R. / Wang, J. / Gogliotti, R.D. / Howard, G.C. / Phan, J. / Acharya, P. / Macdonald, J.D. / Cheng, K. / Lorey, S.L. / Lu, B. / Wenzel, S. / Foshage, A.M. / Alvarado, J. / Wang, F. / ...Authors: Aho, E.R. / Wang, J. / Gogliotti, R.D. / Howard, G.C. / Phan, J. / Acharya, P. / Macdonald, J.D. / Cheng, K. / Lorey, S.L. / Lu, B. / Wenzel, S. / Foshage, A.M. / Alvarado, J. / Wang, F. / Shaw, J.G. / Zhao, B. / Weissmiller, A.M. / Thomas, L.R. / Vakoc, C.R. / Hall, M.D. / Hiebert, S.W. / Liu, Q. / Stauffer, S.R. / Fesik, S.W. / Tansey, W.P.
History
DepositionJul 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2025
Polymers33,5891
Non-polymers6134
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.909, 86.793, 41.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 33589.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Chemical ChemComp-HHM / N-[(3,5-dichlorophenyl)methyl]-3-[(1H-imidazol-1-yl)methyl]benzamide


Mass: 360.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15Cl2N3O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 9905 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 46.35 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.041 / Rrim(I) all: 0.099 / Χ2: 0.924 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.53-2.575.60.5094730.9060.2360.5630.882100
2.57-2.625.70.4264820.9140.1980.4720.932100
2.62-2.675.70.3534770.9460.1610.3890.9399.4
2.67-2.735.60.3374870.9310.1550.3721.0199.4
2.73-2.785.60.2684830.9660.1230.2961.023100
2.78-2.855.70.2424870.9730.1110.2671.002100
2.85-2.925.50.2214880.9740.1020.2440.944100
2.92-35.60.1994780.9720.0920.221.168100
3-3.095.60.1694930.9870.0790.1870.96399.8
3.09-3.195.60.1424920.9840.0650.1560.985100
3.19-3.35.70.134790.9850.060.1441.031100
3.3-3.435.60.1154910.9890.0520.1270.9899.8
3.43-3.595.50.1034960.9930.0480.1140.909100
3.59-3.785.60.0844960.9950.0390.0931.009100
3.78-4.025.50.085020.9930.0370.0880.915100
4.02-4.335.40.0634950.9960.0290.0690.99999.8
4.33-4.765.50.065130.9950.0280.0660.82499.8
4.76-5.455.30.0535050.9970.0250.0590.89499.6
5.45-6.865.20.0535250.9970.0250.0580.64499.6
6.86-504.70.055630.9970.0250.0560.39598.9

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXdev_1760refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHENIXphasing
RefinementResolution: 2.56→43.396 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.2
RfactorNum. reflection% reflection
Rfree0.2303 980 9.94 %
Rwork0.1819 --
obs0.1867 9862 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.86 Å2 / Biso mean: 50.2793 Å2 / Biso min: 26.23 Å2
Refinement stepCycle: final / Resolution: 2.56→43.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 37 38 2439
Biso mean--55.3 44.01 -
Num. residues----305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032495
X-RAY DIFFRACTIONf_angle_d0.7733391
X-RAY DIFFRACTIONf_chiral_restr0.031377
X-RAY DIFFRACTIONf_plane_restr0.003421
X-RAY DIFFRACTIONf_dihedral_angle_d11.283884
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5597-2.69460.2791150.25261024113981
2.6946-2.86340.31941380.257812801418100
2.8634-3.08440.33211420.243212741416100
3.0844-3.39470.23041440.221912861430100
3.3947-3.88560.23891410.189313091450100
3.8856-4.89440.17531470.134513161463100
4.8944-43.40270.21211530.15211393154699
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)
12.1579-0.05880.37031.1581.37022.066-0.04610.0248-0.093-0.2756-0.08240.16910.0282-0.27050.10820.413-0.0639-0.05130.41880.03850.39580.042617.76429.176
22.8380.5521.10711.550.59971.96350.06890.1945-0.25130.02310.0962-0.13750.05180.2215-0.13830.3695-0.0110.01560.39670.00040.367319.89810.622112.4945
33.2024-0.0429-0.59022.7562-0.37972.8394-0.25610.01160.3906-0.12510.1399-0.6782-0.20180.539-0.00770.4662-0.0617-0.04410.5040.02880.465623.06828.482514.2297
43.2307-0.55540.32942.28490.27692.2108-0.1528-0.05830.6512-0.18450.06590.0881-0.44140.0780.05690.4529-0.034-0.0850.30490.02820.41399.161530.653213.3828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 83 )A30 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 209 )A84 - 209
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 233 )A210 - 233
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 334 )A234 - 334

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