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- PDB-2h14: Crystal of WDR5 (apo-form) -

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Basic information

Entry
Database: PDB / ID: 2h14
TitleCrystal of WDR5 (apo-form)
ComponentsWD-repeat protein 5
KeywordsTRANSCRIPTION / histone / beta-propeller / WD-40 repeats / MLL
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
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsCouture, J.F. / Collazo, E. / Trievel, R.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Molecular recognition of histone H3 by the WD40 protein WDR5.
Authors: Couture, J.F. / Collazo, E. / Trievel, R.C.
History
DepositionMay 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD-repeat protein 5


Theoretical massNumber of molelcules
Total (without water)34,7071
Polymers34,7071
Non-polymers00
Water9,566531
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.760, 98.060, 80.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-556-

HOH

Detailsthe protein is a monomer and there is 1 molecule in the AU

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Components

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


Mass: 34707.367 Da / Num. of mol.: 1 / Fragment: Residues 22-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 20-30% PEG 3350 0.1M Hepes 0.05M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.48→28.7 Å / Num. all: 52364 / Num. obs: 50745 / % possible obs: 96.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 5
Reflection shellResolution: 1.48→1.53 Å / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→28.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.726 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.086 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 2578 5.1 %RANDOM
Rwork0.15712 ---
all0.174 50696 --
obs0.15916 48119 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.198 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.48→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 0 531 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222398
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9373256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76125.26993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.179153
X-RAY DIFFRACTIONr_chiral_restr0.0910.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021768
X-RAY DIFFRACTIONr_nbd_refined0.2050.21210
X-RAY DIFFRACTIONr_nbtor_refined0.30.21672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2441
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.259
X-RAY DIFFRACTIONr_mcbond_it0.8771.51539
X-RAY DIFFRACTIONr_mcangle_it1.34122432
X-RAY DIFFRACTIONr_scbond_it2.08231005
X-RAY DIFFRACTIONr_scangle_it2.9984.5824
X-RAY DIFFRACTIONr_rigid_bond_restr1.21132544
X-RAY DIFFRACTIONr_sphericity_free3.2713531
X-RAY DIFFRACTIONr_sphericity_bonded2.32332342
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 165 -
Rwork0.229 2997 -
obs--82.86 %

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