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- PDB-9uk3: Crystal structure of WDR5 in complex with peptide Ac-MRTEPRPPAP-NH2 -

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Basic information

Entry
Database: PDB / ID: 9uk3
TitleCrystal structure of WDR5 in complex with peptide Ac-MRTEPRPPAP-NH2
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: 1.69 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)35,5682
Polymers35,5682
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.072, 80.972, 84.539
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-662-

HOH

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Components

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


Mass: 1177.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / 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.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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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 PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.69→58.48 Å / Num. obs: 31858 / % possible obs: 99.2 % / Redundancy: 9.7 % / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 1.69→1.79 Å / Num. unique obs: 4615 / CC1/2: 0.948

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→58.48 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 1621 5.1 %
Rwork0.1683 --
obs0.1699 31809 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→58.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 0 325 2710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072521
X-RAY DIFFRACTIONf_angle_d0.9813425
X-RAY DIFFRACTIONf_dihedral_angle_d7.735334
X-RAY DIFFRACTIONf_chiral_restr0.063384
X-RAY DIFFRACTIONf_plane_restr0.007429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.3441310.27832480X-RAY DIFFRACTION100
1.74-1.80.29441270.24792511X-RAY DIFFRACTION100
1.8-1.870.23751080.21422516X-RAY DIFFRACTION100
1.87-1.940.2411430.18952490X-RAY DIFFRACTION100
1.94-2.030.22451440.18192486X-RAY DIFFRACTION100
2.03-2.140.21091440.18442521X-RAY DIFFRACTION100
2.14-2.270.21931320.17452523X-RAY DIFFRACTION100
2.27-2.440.23121250.1772520X-RAY DIFFRACTION100
2.44-2.690.23291260.18412560X-RAY DIFFRACTION100
2.69-3.080.20181430.1732534X-RAY DIFFRACTION100
3.08-3.860.16731380.14972355X-RAY DIFFRACTION92
3.89-58.480.16461600.13872692X-RAY DIFFRACTION100

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