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- PDB-9kd4: Structure of WDR5 in complex with WIN motif containing Kif2A 114-120 -

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Basic information

Entry
Database: PDB / ID: 9kd4
TitleStructure of WDR5 in complex with WIN motif containing Kif2A 114-120
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: 1.64 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)70,7244
Polymers70,7244
Non-polymers00
Water5,278293
1
A: WD repeat-containing protein 5
C: Kinesin-like protein KIF2A


Theoretical massNumber of molelcules
Total (without water)35,3622
Polymers35,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 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)35,3622
Polymers35,3622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-4 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.867, 47.271, 129.255
Angle α, β, γ (deg.)90.00, 113.56, 90.00
Int Tables number5
Space group name H-MC121

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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: 715.803 Da / Num. of mol.: 2
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.: 293 / 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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate pH=4, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 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: 1.64→59.24 Å / Num. obs: 78758 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.976 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.077 / Rrim(I) all: 0.144 / Χ2: 0.59 / Net I/σ(I): 4.5 / Num. measured all: 263132
Reflection shellResolution: 1.64→1.73 Å / % possible obs: 99.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.884 / Num. measured all: 32682 / Num. unique obs: 11518 / CC1/2: 0.491 / Rpim(I) all: 0.623 / Rrim(I) all: 1.087 / Χ2: 0.7 / Net I/σ(I) obs: 1.9

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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: 1.64→51.19 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 3904 4.98 %
Rwork0.1777 --
obs0.179 78345 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→51.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4736 0 0 293 5029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134864
X-RAY DIFFRACTIONf_angle_d1.2956624
X-RAY DIFFRACTIONf_dihedral_angle_d7.625656
X-RAY DIFFRACTIONf_chiral_restr0.092755
X-RAY DIFFRACTIONf_plane_restr0.01831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.660.27711030.27262518X-RAY DIFFRACTION93
1.66-1.680.27231380.2642592X-RAY DIFFRACTION97
1.68-1.70.28571310.25582690X-RAY DIFFRACTION98
1.7-1.730.30931400.2382609X-RAY DIFFRACTION99
1.73-1.750.22761430.22762720X-RAY DIFFRACTION99
1.75-1.780.24911320.21582629X-RAY DIFFRACTION100
1.78-1.810.26731450.20672705X-RAY DIFFRACTION100
1.81-1.830.26851380.19382665X-RAY DIFFRACTION100
1.83-1.870.22411370.18542646X-RAY DIFFRACTION100
1.87-1.90.20311400.18722709X-RAY DIFFRACTION99
1.9-1.940.21531450.18222624X-RAY DIFFRACTION99
1.94-1.980.21391350.16852735X-RAY DIFFRACTION100
1.98-2.020.20421370.1642687X-RAY DIFFRACTION100
2.02-2.070.19061250.16712660X-RAY DIFFRACTION99
2.07-2.120.18171620.16792683X-RAY DIFFRACTION100
2.12-2.180.21831320.1592705X-RAY DIFFRACTION100
2.18-2.240.20241380.16522713X-RAY DIFFRACTION100
2.24-2.310.20081430.17762612X-RAY DIFFRACTION98
2.31-2.390.19941270.17822715X-RAY DIFFRACTION100
2.39-2.490.24241390.18222691X-RAY DIFFRACTION100
2.49-2.60.21971180.18182741X-RAY DIFFRACTION100
2.6-2.740.19641360.17622449X-RAY DIFFRACTION90
2.74-2.910.21691550.18012674X-RAY DIFFRACTION100
2.91-3.140.1941510.17962740X-RAY DIFFRACTION100
3.14-3.450.17921540.16612685X-RAY DIFFRACTION100
3.45-3.950.20411400.16732324X-RAY DIFFRACTION85
3.95-4.980.14521480.14022726X-RAY DIFFRACTION100
4.98-51.190.20171720.18242794X-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)
11.44310.1145-0.14691.8702-0.18031.53350.02420.0164-0.08780.0069-0.03860.01410.03510.07970.01420.09350.00730.00580.092-0.02710.071414.7377-9.787645.5394
28.6704-3.2903-0.42552.00292.64756.0982-0.0101-0.78340.23970.7680.029-0.2083-0.22470.1238-0.02420.2531-0.05150.03690.2319-0.03980.22057.7773-3.880256.1247
31.0729-0.26670.16661.5090.48842.0851-0.0170.0067-0.0111-0.0601-0.04450.0767-0.07930.05010.05520.0893-0.01910.01550.06190.01170.087718.018813.04413.4
47.97261.8064-4.89742.0037-6.73562.00290.05850.6280.4618-0.59780.0137-0.0967-0.22520.2359-0.04070.29050.00570.06540.23220.03480.136325.532319.10573.2816
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 120)
3X-RAY DIFFRACTION3(chain 'B' and resid 31 through 334)
4X-RAY DIFFRACTION4(chain 'D' and resid 114 through 120)

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