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- PDB-8hmx: WDR5 in complex with histone H3Q5his peptide -

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Basic information

Entry
Database: PDB / ID: 8hmx
TitleWDR5 in complex with histone H3Q5his peptide
Components
  • WD repeat-containing protein 5
  • histone H3Q5his peptide
KeywordsGENE REGULATION / Histone reader
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
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
Similarity search - Domain/homology
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, H.T. / Zhao, S. / Wang, H.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: WDR5 in complex with histone H3Q5his peptide
Authors: Li, H.T. / Zhao, S. / Wang, H.F.
History
DepositionDec 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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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
B: histone H3Q5his peptide


Theoretical massNumber of molelcules
Total (without water)34,0972
Polymers34,0972
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-2 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.187, 46.857, 65.297
Angle α, β, γ (deg.)90.00, 112.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

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Components

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


Mass: 33492.020 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P61964
#2: Protein/peptide histone H3Q5his peptide


Mass: 604.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic dihydrate (pH 5.5), 22% polyethylene glycol (PEG) 3350, and 0.1% n-Octyl-beta-D-glucoside

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 34866 / % possible obs: 96.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.97 / Χ2: 0.114 / Net I/σ(I): 10.9 / Num. measured all: 122911
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.7-1.7320.48232681.152196.1
1.73-1.7620.4633571.178196.6
1.76-1.7920.38933001.256197.5
1.79-1.831.90.37233591.41197.7
1.83-1.871.90.29533551.493196.9
1.87-1.911.90.24233171.658196.5
1.91-1.961.90.21332481.729195.6
1.96-2.021.80.18332331.944195.4
2.02-2.071.70.16732172.019194.9
2.07-2.141.90.15632952.283195.6
2.14-2.221.80.14132852.42195.8
2.22-2.311.80.13232582.432196.3
2.31-2.411.90.12333552.55196.9
2.41-2.541.90.11633402.848197.5
2.54-2.71.90.10632733.156196.8
2.7-2.911.80.09733313.514196
2.91-3.21.80.09532723.833196.4
3.2-3.661.70.08532594.078194.5
3.66-4.611.70.08532354.308195.1
4.61-501.90.09133884.298198.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9refinement
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→31.96 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1928 1827 5.24 %
Rwork0.1684 --
obs0.1698 34866 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 0 393 2791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062467
X-RAY DIFFRACTIONf_angle_d0.8713347
X-RAY DIFFRACTIONf_dihedral_angle_d12.193878
X-RAY DIFFRACTIONf_chiral_restr0.062378
X-RAY DIFFRACTIONf_plane_restr0.006415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.22741400.20212514X-RAY DIFFRACTION98
1.74-1.790.23631430.1962533X-RAY DIFFRACTION100
1.79-1.850.22591290.18252539X-RAY DIFFRACTION100
1.85-1.920.21181430.16832546X-RAY DIFFRACTION100
1.92-20.20061380.17082537X-RAY DIFFRACTION99
2-2.090.19311560.16782502X-RAY DIFFRACTION99
2.09-2.20.20021310.16512543X-RAY DIFFRACTION99
2.2-2.330.21911380.1752549X-RAY DIFFRACTION99
2.33-2.510.1951190.17832558X-RAY DIFFRACTION100
2.51-2.770.21841270.17572566X-RAY DIFFRACTION99
2.77-3.170.17231410.17412530X-RAY DIFFRACTION99
3.17-3.990.16411570.14792535X-RAY DIFFRACTION98
3.99-31.960.17621650.15552587X-RAY DIFFRACTION98

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