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- PDB-6oi3: Crystal structure of human WDR5 in complex with monomethyl H3R2 p... -

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Basic information

Entry
Database: PDB / ID: 6oi3
TitleCrystal structure of human WDR5 in complex with monomethyl H3R2 peptide
Components
  • Monomethyl H3R2 peptide
  • WD repeat-containing protein 5
KeywordsGENE REGULATION / Methylation / Epigenetics / Post-translational modification / Chromatin / Methylarginine
Function / homology
Function and homology information


Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / MLL1/2 complex / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / nucleosomal DNA binding / regulation of tubulin deacetylation ...Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / MLL1/2 complex / Set1C/COMPASS complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / nucleosomal DNA binding / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / MLL1 complex / regulation of embryonic development / 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 / euchromatin / PKMTs methylate histone lysines / mitotic spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / nucleosome / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cell growth / 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 / 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. / 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 / Histone H3.3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLorton, B.M. / Harijan, R.K. / Burgos, E. / Bonanno, J.B. / Almo, S.C. / Shechter, D.
CitationJournal: Biochemistry / Year: 2020
Title: A Binary Arginine Methylation Switch on Histone H3 Arginine 2 Regulates Its Interaction with WDR5.
Authors: Lorton, B.M. / Harijan, R.K. / Burgos, E.S. / Bonanno, J.B. / Almo, S.C. / Shechter, D.
History
DepositionApr 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: Monomethyl H3R2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2816
Polymers36,9092
Non-polymers3724
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-21 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.294, 98.632, 80.265
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

21A-815-

HOH

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Components

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


Mass: 34390.992 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: Protein/peptide Monomethyl H3R2 peptide


Mass: 2517.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.27 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 100 mM Bis-Tris pH 5.9, 32% PEG3350, 54.6 mM Ammonium Sulfate, 1.67 mM monomethyl H3R2 peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 28, 2017 / Details: KB mirrors
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.66→61.32 Å / Num. obs: 37045 / % possible obs: 100 % / Redundancy: 7.1 % / Rpim(I) all: 0.07 / Net I/σ(I): 8.2
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1856 / Rpim(I) all: 0.34 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H14

2h14


Resolution: 1.66→61.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.077 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 1862 5 %RANDOM
Rwork0.1715 ---
obs0.1731 35159 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.67 Å2 / Biso mean: 14.841 Å2 / Biso min: 6.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 1.66→61.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 23 337 2742
Biso mean--40.23 28.18 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192484
X-RAY DIFFRACTIONr_bond_other_d0.0020.022259
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9463371
X-RAY DIFFRACTIONr_angle_other_deg1.04635270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5375313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14125.21394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48115414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.374153
X-RAY DIFFRACTIONr_chiral_restr0.0850.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022737
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
LS refinement shellResolution: 1.66→1.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 137 -
Rwork0.241 2587 -
all-2724 -
obs--100 %

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