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- PDB-9kd5: Structure of WDR5 in complex with WIN motif containing Kif2A S121G -

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Basic information

Entry
Database: PDB / ID: 9kd5
TitleStructure of WDR5 in complex with WIN motif containing Kif2A S121G
Components
  • Kinesin-like protein KIF2A
  • WD repeat-containing protein 5
KeywordsNUCLEAR PROTEIN / WDR5 / Kif2A / WIN motif / chromatin
Function / homology
Function and homology information


centriolar subdistal appendage / 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 / Kinesins / kinesin complex ...centriolar subdistal appendage / 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 / Kinesins / kinesin complex / microtubule depolymerization / Cardiogenesis / microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / cytoskeletal motor activity / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / : / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / positive regulation of gluconeogenesis / MHC class II antigen presentation / transcription initiation-coupled chromatin remodeling / Resolution of Sister Chromatid Cohesion / regulation of cell migration / mitotic spindle organization / gluconeogenesis / skeletal system development / RHO GTPases Activate Formins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / microtubule cytoskeleton organization / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle pole / mitotic spindle / Separation of Sister Chromatids / nervous system development / HATs acetylate histones / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / microtubule binding / histone binding / microtubule / cell differentiation / regulation of cell cycle / ciliary basal body / nuclear body / cell division / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...: / Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF2A / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, L. / Yang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2025
Title: Crystal structures of Kif2A complexed with WDR5 reveal the structural plasticity of WIN-S7 sites.
Authors: Yang, Y. / Zhang, S. / Wu, Z. / Li, W. / Sun, X. / Xuan, Y. / Hang, T. / Xu, L. / Chen, X.
History
DepositionNov 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 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
C: Kinesin-like protein KIF2A
B: WD repeat-containing protein 5
D: Kinesin-like protein KIF2A


Theoretical massNumber of molelcules
Total (without water)71,0954
Polymers71,0954
Non-polymers00
Water6,521362
1
A: WD repeat-containing protein 5
C: Kinesin-like protein KIF2A


Theoretical massNumber of molelcules
Total (without water)35,5472
Polymers35,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-4 kcal/mol
Surface area11440 Å2
MethodPISA
2
B: WD repeat-containing protein 5
D: Kinesin-like protein KIF2A


Theoretical massNumber of molelcules
Total (without water)35,5472
Polymers35,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-3 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.612, 47.020, 103.488
Angle α, β, γ (deg.)90.00, 107.64, 90.00
Int Tables number4
Space group name H-MP1211

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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 Kinesin-like protein KIF2A / Kinesin-2 / hK2


Mass: 900.983 Da / Num. of mol.: 2 / Mutation: S121G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2A, KIF2, KNS2 / Production host: Escherichia coli (E. coli) / References: UniProt: O00139
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M imidazole malate, pH=5.5, 24% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→49.31 Å / Num. obs: 54747 / % possible obs: 98.9 % / Redundancy: 6.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.052 / Rrim(I) all: 0.132 / Χ2: 1.03 / Net I/σ(I): 11.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 11518 / CC1/2: 0.901 / Rpim(I) all: 0.2 / Rrim(I) all: 0.501 / Χ2: 0.81

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.31 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 2858 5.22 %
Rwork0.1912 --
obs0.1925 54720 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 0 362 5124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054890
X-RAY DIFFRACTIONf_angle_d0.9636654
X-RAY DIFFRACTIONf_dihedral_angle_d7.69658
X-RAY DIFFRACTIONf_chiral_restr0.06756
X-RAY DIFFRACTIONf_plane_restr0.007834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.28481380.25472593X-RAY DIFFRACTION100
1.83-1.860.25281370.22452641X-RAY DIFFRACTION100
1.86-1.90.2141210.20782614X-RAY DIFFRACTION100
1.9-1.940.28821570.25982560X-RAY DIFFRACTION100
1.94-1.980.23481440.20292581X-RAY DIFFRACTION100
1.98-2.030.27641420.20472631X-RAY DIFFRACTION100
2.03-2.080.25431450.20742598X-RAY DIFFRACTION100
2.08-2.130.25371310.21182622X-RAY DIFFRACTION100
2.13-2.20.22091550.1982585X-RAY DIFFRACTION100
2.2-2.270.2961460.25532599X-RAY DIFFRACTION100
2.27-2.350.22541540.20052620X-RAY DIFFRACTION100
2.35-2.440.2321680.1992559X-RAY DIFFRACTION100
2.44-2.550.24221550.19612612X-RAY DIFFRACTION100
2.55-2.690.22581150.1922106X-RAY DIFFRACTION80
2.69-2.860.23271470.1852627X-RAY DIFFRACTION100
2.86-3.080.2111330.18822652X-RAY DIFFRACTION100
3.08-3.390.20641470.17812602X-RAY DIFFRACTION100
3.39-3.880.16091540.16782638X-RAY DIFFRACTION100
3.88-4.880.16911190.14662681X-RAY DIFFRACTION100
4.88-49.310.17311500.18032741X-RAY DIFFRACTION99
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)
10.64570.0356-0.0180.63510.08440.4231-0.0044-0.01580.09420.04880.0198-0.0622-0.00750.0334-0.00070.08870.0013-0.00050.0246-0.00540.138-0.04410.4122-43.6874
24.4583-1.79190.47123.14521.20230.8483-0.035-0.09940.02140.12770.01080.1816-0.0604-0.13580.03990.1243-0.0002-0.01610.08430.0330.1962-12.37616.2747-46.5848
30.3764-0.02560.00560.47070.14780.56540.1355-0.1132-0.1808-0.0457-0.3702-0.4457-0.0253-0.4260.03730.09990.0061-0.00650.3713-0.1707-0.2077-17.043914.0276-5.199
42.75821.751.40023.7440.24381.78970.00980.1437-0.0268-0.20040.0005-0.228-0.00220.18780.00020.11620.0373-0.00920.2098-0.04510.1192-4.213619.3854-3.4592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 31 through 334)
2X-RAY DIFFRACTION2(chain 'C' and resid 114 through 121)
3X-RAY DIFFRACTION3(chain 'B' and resid 31 through 334)
4X-RAY DIFFRACTION4(chain 'D' and resid 114 through 121)

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