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- PDB-8wxu: Structure of WDR5 in complex with WIN motif containing MBD3C C44S... -

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Basic information

Entry
Database: PDB / ID: 8wxu
TitleStructure of WDR5 in complex with WIN motif containing MBD3C C44S/R45E/V46G
Components
  • MBD3C
  • WD repeat-containing protein 5
KeywordsNUCLEAR PROTEIN / WDR5 / MBD3C / WIN motif / chromatin
Function / homology
Function and homology information


histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / mitotic spindle / HATs acetylate histones / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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
WDR5 beta-propeller domain / 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. / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsXu, L. / Yang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural studies of WDR5 in complex with MBD3C WIN motif reveal a unique binding mode.
Authors: Yang, Y. / Xu, L. / Zhang, S. / Yao, L. / Ding, Y. / Li, W. / Chen, X.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: WD repeat-containing protein 5
D: MBD3C


Theoretical massNumber of molelcules
Total (without water)35,8112
Polymers35,8112
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-9 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.694, 98.917, 79.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 34646.309 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 MBD3C


Mass: 1164.207 Da / Num. of mol.: 1 / Mutation: C44S,R45E,V46G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M lithium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 12679 / % possible obs: 98.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.15
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.513 / Num. unique obs: 640

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALAdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→39.9 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2334 1272 10.62 %
Rwork0.1776 --
obs0.1836 11979 92.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 0 98 2516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042488
X-RAY DIFFRACTIONf_angle_d0.8033375
X-RAY DIFFRACTIONf_dihedral_angle_d6.943329
X-RAY DIFFRACTIONf_chiral_restr0.055379
X-RAY DIFFRACTIONf_plane_restr0.005421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.470.3171010.2154849X-RAY DIFFRACTION68
2.47-2.580.31291210.21821041X-RAY DIFFRACTION83
2.58-2.720.28331350.20151181X-RAY DIFFRACTION93
2.72-2.880.30021600.20291254X-RAY DIFFRACTION98
2.89-3.110.25291440.19721256X-RAY DIFFRACTION99
3.11-3.420.24911400.19131269X-RAY DIFFRACTION99
3.42-3.920.23541640.17071270X-RAY DIFFRACTION99
3.92-4.930.19041460.1391279X-RAY DIFFRACTION98
4.93-39.90.18411610.1731308X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8631-0.1031-0.1860.84920.3622.48790.00850.0910.2053-0.05920.0053-0.062-0.17620.1083-0.00180.218-0.00920.00460.15570.02150.1988-21.2093-15.99234.8592
27.6457-5.6409-2.91256.28753.92797.3059-0.15820.1471-0.4382-0.58870.016-0.28670.03290.28750.09580.3808-0.0949-0.04740.25540.00840.4937-23.7016-30.00946.4461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 31 through 334)
2X-RAY DIFFRACTION2(chain 'D' and resid 40 through 48)

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