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- PDB-2h9m: WDR5 in complex with unmodified H3K4 peptide -

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Basic information

Entry
Database: PDB / ID: 2h9m
TitleWDR5 in complex with unmodified H3K4 peptide
Components
  • H3 histoneHistone H3
  • WD-repeat protein 5WD40 repeat
Keywordsstructural genomics / gene regulation / wdr5 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / : / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / : / NoRC negatively regulates rRNA expression / : / Transcriptional regulation by small RNAs ...Factors involved in megakaryocyte development and platelet production / : / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / : / NoRC negatively regulates rRNA expression / : / Transcriptional regulation by small RNAs / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / 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 / structural constituent of chromatin / nucleosome / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / protein heterodimerization activity / 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 / DNA binding / nucleoplasm / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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
WD repeat-containing protein 5 / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMin, J.R. / Schuetz, A. / Allali-Hassani, A. / Martin, F. / Loppnau, P. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. ...Min, J.R. / Schuetz, A. / Allali-Hassani, A. / Martin, F. / Loppnau, P. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: Embo J. / Year: 2006
Title: Structural basis for molecular recognition and presentation of histone H3 By WDR5.
Authors: Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Vedadi, M. / Bochkarev, A. / Plotnikov, A.N. / Arrowsmith, C.H. / Min, J.
History
DepositionJun 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 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, 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

Downloads & links

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Assembly

Deposited unit
A: WD-repeat protein 5
B: H3 histone
C: WD-repeat protein 5
D: H3 histone


Theoretical massNumber of molelcules
Total (without water)71,2574
Polymers71,2574
Non-polymers00
Water8,485471
1
A: WD-repeat protein 5
B: H3 histone


Theoretical massNumber of molelcules
Total (without water)35,6282
Polymers35,6282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-3 kcal/mol
Surface area11910 Å2
MethodPISA
2
C: WD-repeat protein 5
D: H3 histone


Theoretical massNumber of molelcules
Total (without water)35,6282
Polymers35,6282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-2 kcal/mol
Surface area11880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.951, 61.375, 64.739
Angle α, β, γ (deg.)110.34, 91.22, 112.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein WD-repeat protein 5 / WD40 repeat / BMP2-induced 3-kb gene protein / WDR5


Mass: 34376.969 Da / Num. of mol.: 2
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: Protein/peptide H3 histone / Histone H3


Mass: 1251.436 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Xenopus tropicalis (Western clawed frog).
References: UniProt: Q6P823
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M di-Na Tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 1, 2006
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→59.76 Å / Num. all: 44230 / Num. obs: 44230 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 73.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→59.76 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.006 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25701 2253 5.1 %RANDOM
Rwork0.20393 ---
all0.20656 41975 --
obs0.20656 41975 90.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.176 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.69 Å20.35 Å2
2--1.57 Å20.76 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 0 471 5270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224911
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9396659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99625.054186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06715852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.214158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023598
X-RAY DIFFRACTIONr_nbd_refined0.1890.22320
X-RAY DIFFRACTIONr_nbtor_refined0.2930.23319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2492
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.227
X-RAY DIFFRACTIONr_mcbond_it0.4551.53164
X-RAY DIFFRACTIONr_mcangle_it0.77624974
X-RAY DIFFRACTIONr_scbond_it1.03232049
X-RAY DIFFRACTIONr_scangle_it1.5874.51685
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 129 -
Rwork0.26 2347 -
obs--68.53 %

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