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- PDB-8wxr: Structure of WDR5 in complex with WIN motif containing MBD3C F47A -

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Basic information

Entry
Database: PDB / ID: 8wxr
TitleStructure of WDR5 in complex with WIN motif containing MBD3C F47A
Components
  • MBD3C
  • WD repeat-containing protein 5
KeywordsNUCLEAR PROTEIN / WDR5 / MBD3C / WIN motif / chromatin
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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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
B: WD repeat-containing protein 5
D: MBD3C


Theoretical massNumber of molelcules
Total (without water)71,6414
Polymers71,6414
Non-polymers00
Water6,900383
1
A: WD repeat-containing protein 5
C: MBD3C


Theoretical massNumber of molelcules
Total (without water)35,8212
Polymers35,8212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-5 kcal/mol
Surface area11830 Å2
MethodPISA
2
B: WD repeat-containing protein 5
D: MBD3C


Theoretical massNumber of molelcules
Total (without water)35,8212
Polymers35,8212
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.697, 47.028, 103.050
Angle α, β, γ (deg.)90.00, 107.47, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 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 MBD3C


Mass: 1174.335 Da / Num. of mol.: 2 / Mutation: F47A
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.: 383 / 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: 2.09 Å3/Da / Density % sol: 41.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium dihydrogen phosphate, 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: 2.08→50 Å / Num. obs: 31841 / % possible obs: 90.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.52
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.181 / Num. unique obs: 1443

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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: 2.08→12.65 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1986 3103 9.75 %
Rwork0.1527 --
obs0.1572 31827 89.58 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.08→12.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 0 383 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084910
X-RAY DIFFRACTIONf_angle_d1.0226664
X-RAY DIFFRACTIONf_dihedral_angle_d7.679651
X-RAY DIFFRACTIONf_chiral_restr0.063758
X-RAY DIFFRACTIONf_plane_restr0.006827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.120.2215780.1667892X-RAY DIFFRACTION60
2.12-2.150.23291220.15751196X-RAY DIFFRACTION82
2.15-2.190.25021280.15881171X-RAY DIFFRACTION83
2.19-2.230.22771320.15771220X-RAY DIFFRACTION83
2.23-2.270.23071330.15851201X-RAY DIFFRACTION85
2.27-2.320.23391260.15851234X-RAY DIFFRACTION85
2.32-2.370.20831240.15081295X-RAY DIFFRACTION88
2.37-2.420.22751320.15981261X-RAY DIFFRACTION87
2.42-2.480.23471420.16491281X-RAY DIFFRACTION88
2.48-2.550.21891490.1631269X-RAY DIFFRACTION90
2.55-2.620.22241310.16181328X-RAY DIFFRACTION90
2.62-2.710.21351250.16161320X-RAY DIFFRACTION91
2.71-2.80.2331600.16181345X-RAY DIFFRACTION93
2.8-2.910.21321690.16641342X-RAY DIFFRACTION94
2.91-3.040.23331280.16811376X-RAY DIFFRACTION94
3.04-3.20.20451700.15641404X-RAY DIFFRACTION96
3.2-3.40.18341430.15041423X-RAY DIFFRACTION97
3.4-3.660.18291530.14631427X-RAY DIFFRACTION98
3.66-4.010.17311790.13641415X-RAY DIFFRACTION98
4.01-4.570.15531890.13021392X-RAY DIFFRACTION96
4.57-5.670.16271300.14011484X-RAY DIFFRACTION98
5.67-12.650.18291600.16161448X-RAY DIFFRACTION95
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)
11.3245-0.16470.06841.6403-0.04191.29130.07110.0726-0.0196-0.0897-0.09320.02970.0337-0.18450.01620.07750.0005-0.00420.1377-0.01220.0653-17.057311.6157-5.2152
26.92461.84041.81985.238-1.66325.85620.04570.2478-0.3082-0.29410.0778-0.71110.34030.7986-0.11960.13320.0486-0.01070.2712-0.04070.2185-3.079716.2946-3.718
32.06940.5027-0.15951.90440.54051.48950.03760.03240.07670.094-0.02430.03830.02840.0206-0.00890.07360.01330.00280.05390.01280.115-0.04718.0544-43.6635
45.4177-3.68123.27848.5827-0.17235.293-0.0737-0.20680.10810.4616-0.01160.6278-0.2661-0.60350.08290.13180.0349-0.00010.12840.04760.2791-12.789913.6864-46.4128
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)
3X-RAY DIFFRACTION3(chain 'B' and resid 31 through 334)
4X-RAY DIFFRACTION4(chain 'D' and resid 40 through 47)

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