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- PDB-9uk1: Crystal structure of WDR5 in complex with EMBOW -

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Basic information

Entry
Database: PDB / ID: 9uk1
TitleCrystal structure of WDR5 in complex with EMBOW
Components
  • SCRIB overlapping open reading frame protein
  • WD repeat-containing protein 5
KeywordsNUCLEAR PROTEIN / WD-repeat / WIN site / MLL complex
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 / negative regulation of translational initiation / 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
SCRIB overlapping open reading frame protein / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsMin, J.-R. / Zhang, M. / Chen, M.-X.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Cell Chem Biol / Year: 2025
Title: Therapeutic targeting of WDR5-MLL1 by EMBOW-derived peptides suppresses leukemia progression.
Authors: Zhang, M. / Chen, M. / Li, P. / Min, J.
History
DepositionApr 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: SCRIB overlapping open reading frame protein
A: WD repeat-containing protein 5


Theoretical massNumber of molelcules
Total (without water)46,3932
Polymers46,3932
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-5 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.004, 81.043, 108.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-465-

HOH

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Components

#1: Protein SCRIB overlapping open reading frame protein / oSCRIB


Mass: 12002.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EMBOW / Source: (gene. exp.) Homo sapiens (human) / Gene: SCRIB / Production host: Escherichia coli (E. coli) / References: UniProt: C0HLS1
#2: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 34390.992 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium tartrate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350, pH7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.02→64.94 Å / Num. obs: 27509 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.995 / Net I/σ(I): 9.9
Reflection shellResolution: 2.02→2.13 Å / Num. unique obs: 3922 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→46 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 23.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1342 4.9 %
Rwork0.1914 --
obs0.1931 27395 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 0 163 2533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072503
X-RAY DIFFRACTIONf_angle_d0.9283397
X-RAY DIFFRACTIONf_dihedral_angle_d7.239328
X-RAY DIFFRACTIONf_chiral_restr0.063382
X-RAY DIFFRACTIONf_plane_restr0.007423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.090.34611250.27832504X-RAY DIFFRACTION98
2.09-2.170.27921380.25522547X-RAY DIFFRACTION100
2.17-2.270.30061320.24782594X-RAY DIFFRACTION100
2.27-2.390.25751380.23922547X-RAY DIFFRACTION100
2.39-2.540.27551430.22832591X-RAY DIFFRACTION100
2.54-2.740.2721300.20552588X-RAY DIFFRACTION100
2.74-3.010.23911300.19872603X-RAY DIFFRACTION100
3.01-3.450.20921330.17552622X-RAY DIFFRACTION100
3.45-4.340.19481490.15612644X-RAY DIFFRACTION100
4.35-460.17061240.16432813X-RAY DIFFRACTION100

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