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- PDB-8wxx: Structure of WDR5 in complex with WIN motif containing SET1B E175... -

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Basic information

Entry
Database: PDB / ID: 8wxx
TitleStructure of WDR5 in complex with WIN motif containing SET1B E1750R/G1751V
Components
  • SET1B
  • 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
B: WD repeat-containing protein 5
C: SET1B
D: SET1B


Theoretical massNumber of molelcules
Total (without water)71,6154
Polymers71,6154
Non-polymers00
Water7,044391
1
A: WD repeat-containing protein 5
D: SET1B


Theoretical massNumber of molelcules
Total (without water)35,8082
Polymers35,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10 kcal/mol
Surface area11800 Å2
MethodPISA
2
B: WD repeat-containing protein 5
C: SET1B


Theoretical massNumber of molelcules
Total (without water)35,8082
Polymers35,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.801, 47.244, 129.675
Angle α, β, γ (deg.)90.00, 112.97, 90.00
Int Tables number5
Space group name H-MC121

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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 SET1B


Mass: 1161.335 Da / Num. of mol.: 2 / Mutation: E1750R, G1751V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate, pH 5.5, 16% PEG 4000, 10% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37965 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.35
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.474 / Num. unique obs: 1855

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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: 2.1→27.21 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 3654 9.63 %
Rwork0.1737 --
obs0.1772 37928 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→27.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 0 391 5216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074943
X-RAY DIFFRACTIONf_angle_d1.1276697
X-RAY DIFFRACTIONf_dihedral_angle_d7.699650
X-RAY DIFFRACTIONf_chiral_restr0.086754
X-RAY DIFFRACTIONf_plane_restr0.006830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.30551360.2591280X-RAY DIFFRACTION95
2.13-2.150.27221270.24891307X-RAY DIFFRACTION98
2.15-2.190.30061420.24751253X-RAY DIFFRACTION98
2.19-2.220.28741710.23791263X-RAY DIFFRACTION98
2.22-2.250.28161250.24111281X-RAY DIFFRACTION97
2.25-2.290.28561520.23551294X-RAY DIFFRACTION99
2.29-2.330.2581350.22461297X-RAY DIFFRACTION98
2.33-2.370.26721480.21761306X-RAY DIFFRACTION99
2.37-2.420.24781330.2071324X-RAY DIFFRACTION99
2.42-2.470.22191480.20071314X-RAY DIFFRACTION99
2.47-2.520.24241660.19821281X-RAY DIFFRACTION99
2.52-2.580.2211480.19471291X-RAY DIFFRACTION99
2.58-2.640.24591450.18791311X-RAY DIFFRACTION100
2.64-2.710.21831310.17821351X-RAY DIFFRACTION100
2.71-2.790.2151560.18091289X-RAY DIFFRACTION100
2.79-2.880.22011320.17731334X-RAY DIFFRACTION100
2.88-2.990.21541260.16951356X-RAY DIFFRACTION100
2.99-3.110.19031270.16841324X-RAY DIFFRACTION100
3.11-3.250.20321520.15691329X-RAY DIFFRACTION100
3.25-3.420.18831480.15591322X-RAY DIFFRACTION100
3.42-3.630.18171450.14321360X-RAY DIFFRACTION100
3.63-3.910.17411190.14451347X-RAY DIFFRACTION100
3.91-4.30.14881320.13291348X-RAY DIFFRACTION100
4.3-4.920.14911290.1261348X-RAY DIFFRACTION100
4.93-6.190.22781190.16911394X-RAY DIFFRACTION100
6.19-27.210.20381620.17451370X-RAY DIFFRACTION98
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)
13.1112-0.7475-0.73182.6080.39182.64820.02890.003-0.1295-0.0725-0.05290.05370.0304-0.17020.02890.2032-0.00730.01280.18130.03990.10917.752712.314313.8104
21.73260.5264-0.2142.3587-0.58152.90080.01080.1001-0.035-0.163-0.0565-0.2354-0.2139-0.02270.05160.17780.04560.02920.1007-0.00830.168314.741335.51746.0992
34.0921-1.5012-0.24492.0052-3.65754.938-0.0315-0.37040.16220.6525-0.0697-0.1778-0.4186-0.19570.12660.31170.0636-0.00060.2006-0.04290.20688.050140.231157.2901
45.3734-3.9505-3.83452.00298.16786.3543-0.06130.69390.1139-1.36670.16560.0178-0.7223-0.0562-0.13480.4315-0.04010.03210.28810.0610.207623.849516.83732.2176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 32 through 334)
2X-RAY DIFFRACTION2(chain 'B' and resid 32 through 334)
3X-RAY DIFFRACTION3(chain 'C' and resid 1745 through 1753)
4X-RAY DIFFRACTION4(chain 'D' and resid 1745 through 1753)

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