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- PDB-4qqe: Crystal structure of WDR5, WD repeat domain 5 in complex with com... -

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Basic information

Entry
Database: PDB / ID: 4qqe
TitleCrystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION / WDR5 / Structural Genomics / Structural Genomics Consortium / SGC
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 ...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 / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / 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
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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-37F / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDong, A. / Dombrovski, L. / Wernimont, A. / Smil, D. / Getlik, M. / Senisterra, G. / Poda, G. / Al-Awar, R. / Bountra, C. / Arrowsmith, C.H. ...Dong, A. / Dombrovski, L. / Wernimont, A. / Smil, D. / Getlik, M. / Senisterra, G. / Poda, G. / Al-Awar, R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Schapira, M. / Vedadi, M. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of WDR5, WD repeat domain 5 in complex with compound SGC-DS-MT-0345
Authors: Dombrovski, L. / Dong, A. / Wernimont, A. / Smil, D. / Getlik, M. / Senisterra, G. / Poda, G. / Al-Awar, R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Schapira, M. / Vedadi, M. / Wu, H.
History
DepositionJun 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references / Source and taxonomy
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)35,01913
Polymers34,2901
Non-polymers72912
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.896, 85.267, 40.209
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 34289.887 Da / Num. of mol.: 1 / Fragment: UNP residues 24-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIG3, WDR5 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)V2RpRARE / References: UniProt: P61964

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Non-polymers , 5 types, 229 molecules

#2: Chemical ChemComp-37F / N-[2-(4-methylpiperazin-1-yl)-5-(quinolin-3-yl)phenyl]-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide


Mass: 507.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24F3N5O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97959 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 1, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 26561 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.107 / Χ2: 1.226 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.837.60.87213080.8111100
1.83-1.867.80.73312830.831100
1.86-1.97.80.64913000.8521100
1.9-1.947.90.53713150.9041100
1.94-1.987.90.45212950.9971100
1.98-2.037.90.39113231.0051100
2.03-2.087.90.34512991.0651100
2.08-2.137.90.29613191.1151100
2.13-2.27.90.24313071.1511100
2.2-2.277.90.22813001.1691100
2.27-2.357.90.19413251.0641100
2.35-2.447.90.1613171.0661100
2.44-2.557.90.1513241.0941100
2.55-2.697.90.12813361.3521100
2.69-2.867.90.11213301.5221100
2.86-3.087.80.09213281.6191100
3.08-3.397.80.06713501.581100
3.39-3.887.80.05513521.6271100
3.88-4.887.60.04413721.651199.9
4.88-507.10.0514781.977199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Coot0.7.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IA9

4ia9


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.241 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 862 3.3 %RANDOM
Rwork0.1734 ---
obs0.1749 26454 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.07 Å2 / Biso mean: 23.283 Å2 / Biso min: 14.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.53 Å2-0 Å2-0 Å2
2---1.45 Å20 Å2
3---3.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 57 217 2589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022475
X-RAY DIFFRACTIONr_bond_other_d0.0020.022268
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9553382
X-RAY DIFFRACTIONr_angle_other_deg0.8263.0055244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2455319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73525.32692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96715393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.489152
X-RAY DIFFRACTIONr_chiral_restr0.0780.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_mcbond_it1.1472.2531240
X-RAY DIFFRACTIONr_mcbond_other1.1472.2511239
X-RAY DIFFRACTIONr_mcangle_it1.6913.3751556
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 62 -
Rwork0.239 1798 -
all-1860 -
obs--96.57 %

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