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- PDB-8wxt: Structure of WDR5 in complex with WIN motif containing MBD3C R45E/V46G -

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Basic information

Entry
Database: PDB / ID: 8wxt
TitleStructure of WDR5 in complex with WIN motif containing MBD3C 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 / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / Neddylation / HATs acetylate histones / 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: 1.83 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
A: WD repeat-containing protein 5
C: MBD3C


Theoretical massNumber of molelcules
Total (without water)35,8272
Polymers35,8272
Non-polymers00
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-10 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.442, 98.831, 80.178
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: 1180.272 Da / Num. of mol.: 1 / Mutation: 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.: 340 / 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: 43.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M imidazole malate, pH 5.5, 33% PEG 600

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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: 1.83→50 Å / Num. obs: 27245 / % possible obs: 97.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 32.53
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.324 / Num. unique obs: 1394

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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: 1.83→6.87 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 1324 4.86 %
Rwork0.1509 --
obs0.1523 27227 99.84 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→6.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 0 340 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062482
X-RAY DIFFRACTIONf_angle_d0.9383367
X-RAY DIFFRACTIONf_dihedral_angle_d7.516329
X-RAY DIFFRACTIONf_chiral_restr0.063379
X-RAY DIFFRACTIONf_plane_restr0.007419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90.21281360.17762870X-RAY DIFFRACTION100
1.9-1.990.21731460.15422832X-RAY DIFFRACTION100
1.99-2.090.18821290.15492865X-RAY DIFFRACTION100
2.09-2.210.1991720.14842835X-RAY DIFFRACTION100
2.21-2.380.16421330.15392873X-RAY DIFFRACTION100
2.38-2.610.18971540.16392875X-RAY DIFFRACTION100
2.61-2.960.19841480.15892877X-RAY DIFFRACTION100
2.96-3.630.15711540.14022913X-RAY DIFFRACTION100
3.63-6.870.1591520.14112963X-RAY DIFFRACTION99
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)
11.9116-0.0012-0.21471.0018-0.22211.95870.0291-0.02430.12010.0223-0.02320.0711-0.1073-0.1036-0.00470.0734-0.00610.0060.038-0.01190.0722-18.1276-15.9909-4.9547
22-2.8703-6.67679.73880.69197.7901-0.3552-0.1453-0.92910.03030.09550.16780.9611-0.4550.25970.19-0.0267-0.02930.1792-0.01660.1746-15.6281-29.9057-6.7016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 31 through 334)
2X-RAY DIFFRACTION2(chain 'C' and resid 40 through 48)

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