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- PDB-9kfn: Structure of WDR5 in complex with mutated EMBOW T3V -

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Basic information

Entry
Database: PDB / ID: 9kfn
TitleStructure of WDR5 in complex with mutated EMBOW T3V
Components
  • EMBOW
  • WD repeat-containing protein 5
KeywordsNUCLEAR PROTEIN / WDR5 / EMBOW / 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: 2.8 Å
AuthorsXu, L. / Yang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of WDR5 in complex with mutated EMBOW T3V
Authors: Xu, L. / Yang, Y.
History
DepositionNov 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,4352
Polymers35,4352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.112, 126.112, 38.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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 EMBOW


Mass: 788.958 Da / Num. of mol.: 1 / Mutation: T3V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M imidazole malate, pH 8.5, 12.5 % (w/v) PEG 10000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→38.96 Å / Num. obs: 8642 / % possible obs: 96.1 % / Redundancy: 16.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.037 / Rrim(I) all: 0.147 / Χ2: 1.09 / Net I/σ(I): 16.3 / Num. measured all: 142399
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 100 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.904 / Num. measured all: 22519 / Num. unique obs: 1294 / CC1/2: 0.962 / Rpim(I) all: 0.222 / Rrim(I) all: 0.932 / Χ2: 0.79 / Net I/σ(I) obs: 5.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
PROCORdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→31.53 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 438 5.11 %
Rwork0.1934 --
obs0.1959 8572 95.52 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→31.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 0 0 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042440
X-RAY DIFFRACTIONf_angle_d0.7943319
X-RAY DIFFRACTIONf_dihedral_angle_d6.94324
X-RAY DIFFRACTIONf_chiral_restr0.053378
X-RAY DIFFRACTIONf_plane_restr0.006415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.32831510.25452781X-RAY DIFFRACTION100
3.21-4.040.30921160.22952463X-RAY DIFFRACTION87
4.04-31.530.18871710.15832890X-RAY DIFFRACTION100
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)
14.4825-1.59360.20482.52830.17842.7871-0.0579-0.03340.63610.06720.0375-0.3381-0.30630.0006-0.01380.3816-0.0382-0.02320.29860.02180.353818.586836.6796-9.1795
22.16571.50411.11282.88891.84843.47250.1368-0.52460.04560.3606-0.2572-0.3516-0.07230.682-0.07490.6456-0.0701-0.14380.8091-0.10240.687621.9739.61764.4641
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 1 through 6)

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