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- PDB-9iy5: WDR5 inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 9iy5
TitleWDR5 inhibitor complex
Components
  • WD repeat-containing protein 5
  • YCP-A1EAK-A1ECH
KeywordsSTRUCTURAL PROTEIN / WDR5
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 / skeletal system development / gluconeogenesis / 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 / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / regulation of cell cycle / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, F. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: WDR5 inhibitor complex structure
Authors: Wang, F. / Zhou, C.
History
DepositionJul 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
C: YCP-A1EAK-A1ECH
D: YCP-A1EAK-A1ECH


Theoretical massNumber of molelcules
Total (without water)74,1564
Polymers74,1564
Non-polymers00
Water11,548641
1
A: WD repeat-containing protein 5
C: YCP-A1EAK-A1ECH


Theoretical massNumber of molelcules
Total (without water)37,0782
Polymers37,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
D: YCP-A1EAK-A1ECH


Theoretical massNumber of molelcules
Total (without water)37,0782
Polymers37,0782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.030, 61.447, 64.716
Angle α, β, γ (deg.)68.48, 88.73, 67.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein WD repeat-containing protein 5 / BMP2-induced 3-kb gene protein


Mass: 36635.438 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 YCP-A1EAK-A1ECH


Mass: 442.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: Bis-tris pH 5.5 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→37.45 Å / Num. obs: 155092 / % possible obs: 94.97 % / Redundancy: 3.5 % / CC1/2: 0.966 / Rmerge(I) obs: 0.1683 / Net I/σ(I): 4.48
Reflection shellResolution: 1.6→1.62 Å / Rmerge(I) obs: 0.5024 / Num. unique obs: 5002 / CC1/2: 0.857

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_4924: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UVM

3uvm


Resolution: 1.8→37.45 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 5301 4.85 %
Rwork0.2213 --
obs0.223 109323 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4671 0 64 641 5376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.073
X-RAY DIFFRACTIONf_dihedral_angle_d14.289659
X-RAY DIFFRACTIONf_chiral_restr0.069748
X-RAY DIFFRACTIONf_plane_restr0.007818
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.31891640.29013394X-RAY DIFFRACTION94
1.82-1.840.29961480.26943469X-RAY DIFFRACTION95
1.84-1.860.26641990.2443407X-RAY DIFFRACTION95
1.86-1.890.2761630.24353413X-RAY DIFFRACTION94
1.89-1.910.29161600.22873424X-RAY DIFFRACTION95
1.91-1.940.30592060.22423392X-RAY DIFFRACTION95
1.94-1.970.24941710.23013506X-RAY DIFFRACTION94
1.97-20.2451830.22253336X-RAY DIFFRACTION94
2-2.030.26621700.22823521X-RAY DIFFRACTION95
2.03-2.060.25271760.22653460X-RAY DIFFRACTION95
2.06-2.10.27261700.2223434X-RAY DIFFRACTION95
2.1-2.130.27682090.22773445X-RAY DIFFRACTION94
2.13-2.180.25941400.22093455X-RAY DIFFRACTION96
2.18-2.220.26231920.21993440X-RAY DIFFRACTION95
2.22-2.270.292040.23083469X-RAY DIFFRACTION95
2.27-2.320.31861710.23323502X-RAY DIFFRACTION96
2.32-2.380.32882120.23253471X-RAY DIFFRACTION96
2.38-2.440.28361810.23953436X-RAY DIFFRACTION96
2.44-2.510.32811380.23163507X-RAY DIFFRACTION96
2.51-2.60.25261570.23893559X-RAY DIFFRACTION96
2.6-2.690.27341580.22483520X-RAY DIFFRACTION96
2.69-2.80.22541840.23113513X-RAY DIFFRACTION96
2.8-2.920.25931780.22153500X-RAY DIFFRACTION96
2.92-3.080.26741630.22983514X-RAY DIFFRACTION97
3.08-3.270.2412360.22773437X-RAY DIFFRACTION97
3.27-3.520.24822130.20093440X-RAY DIFFRACTION96
3.52-3.880.21241830.19653493X-RAY DIFFRACTION96
3.88-4.440.21581690.18783521X-RAY DIFFRACTION97
4.44-5.590.20251420.20493546X-RAY DIFFRACTION96
5.59-37.450.22491610.22573498X-RAY DIFFRACTION96
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)
11.7512-0.5791-0.54751.32770.36411.0205-0.00630.0110.1061-0.0840.0430.00820.0156-0.0556-0.03950.081-0.0171-0.01020.11470.02340.069713.1284-3.752813.2704
23.1243-0.2340.47542.42520.80883.09710.0051-0.2021-0.17730.09190.06660.270.3114-0.2267-0.0680.1003-0.0142-0.0060.11150.03440.1266-1.6748-13.305822.3403
31.99130.9211-0.79382.24510.13661.8443-0.0694-0.2933-0.1753-0.0212-0.01130.07490.1985-0.06990.07210.1220.0281-0.0040.16590.05870.116514.2944-22.166220.7261
41.67110.16980.03421.39580.56581.56890.0102-0.0897-0.03030.09840.0858-0.16510.00940.2752-0.09010.08710.0155-0.00520.12890.00930.099639.8898-21.4784-8.4937
51.93-0.20790.04491.53530.65712.859-0.04930.0837-0.09340.02560.00840.0181-0.0039-0.22670.02610.0580.00110.00390.12930.02430.090422.1195-22.0967-15.9945
62.07810.9233-0.65582.8831-0.76352.02220.07390.32390.2331-0.05370.0340.3038-0.586-0.5062-0.11310.25010.0684-0.00090.27010.03250.133320.9996-6.961-19.2586
71.6267-0.1075-0.02391.2443-0.37061.9745-0.04080.19890.2333-0.18010.1115-0.1638-0.49510.2999-0.04860.2658-0.08210.04720.22470.0150.170539.2565-4.815-15.428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 167 )
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 233 )
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 334 )
4X-RAY DIFFRACTION4chain 'B' and (resid 31 through 126 )
5X-RAY DIFFRACTION5chain 'B' and (resid 127 through 199 )
6X-RAY DIFFRACTION6chain 'B' and (resid 200 through 252 )
7X-RAY DIFFRACTION7chain 'B' and (resid 253 through 334 )

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