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- PDB-9ikb: Crystal structure of heterotrimeric Kinesin-2 -

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Basic information

Entry
Database: PDB / ID: 9ikb
TitleCrystal structure of heterotrimeric Kinesin-2
Components
  • Kinesin-associated protein
  • Kinesin-like protein
  • Kinesin-like protein klp-20
KeywordsTRANSPORT PROTEIN / Kineisin
Function / homology
Function and homology information


axonemal heterotrimeric kinesin-II complex / kinesin II complex / negative regulation of non-motile cilium assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / ciliary transition zone / cilium organization ...axonemal heterotrimeric kinesin-II complex / kinesin II complex / negative regulation of non-motile cilium assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Intraflagellar transport / intraciliary anterograde transport / positive regulation of non-motile cilium assembly / ciliary transition zone / cilium organization / anterograde axonal transport / non-motile cilium / kinesin complex / microtubule motor activity / microtubule-based movement / kinesin binding / axoneme / cilium assembly / axon cytoplasm / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / 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-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / 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 / Armadillo/beta-catenin-like repeats / Armadillo / Kinesin motor domain superfamily / Armadillo-like helical / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-associated protein / Kinesin-like protein / Kinesin-like protein klp-20
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.54 Å
AuthorsRen, J. / Zhao, L. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971160,5242021 China
CitationJournal: To Be Published
Title: Crystal structure of heterotrimeric Kinesin-2
Authors: Ren, J. / Zhao, L. / Feng, W.
History
DepositionJun 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Kinesin-like protein
C: Kinesin-like protein klp-20
G: Kinesin-associated protein


Theoretical massNumber of molelcules
Total (without water)108,9343
Polymers108,9343
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, the molecular mass of the complex was determined by SEC-MALS.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.445, 107.445, 255.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Kinesin-like protein / Kinesin-like protein klp-11


Mass: 28119.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: klp-11, CELE_F20C5.2, F20C5.2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q19633
#2: Protein Kinesin-like protein klp-20


Mass: 13985.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: klp-20, Y50D7A.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q965T6
#3: Protein Kinesin-associated protein


Mass: 66828.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: kap-1, CELE_F08F8.3, F08F8.3 / Production host: Escherichia coli (E. coli) / References: UniProt: H2KZP1
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: 3.38 Å3/Da / Density % sol: 63.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 22%(w/v) PEG3350, 0.2M Sodium malonate / PH range: 6.4-7.6

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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: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.54→37.6 Å / Num. obs: 17828 / % possible obs: 93.8 % / Redundancy: 13.3 % / CC1/2: 0.999 / CC star: 0.999 / Net I/σ(I): 15.3
Reflection shellResolution: 3.54→3.73 Å / Redundancy: 12.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1558 / CC1/2: 0.75 / CC star: 0.75 / % possible all: 57.7

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
HKL-2000v1.0data scaling
HKL-2000v1.0data reduction
PHASERv2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.54→37.57 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2705 863 4.84 %Random selectioin
Rwork0.2297 ---
obs0.2317 17828 93.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137 Å2
Refinement stepCycle: LAST / Resolution: 3.54→37.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6109 0 0 0 6109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026205
X-RAY DIFFRACTIONf_angle_d0.5128384
X-RAY DIFFRACTIONf_dihedral_angle_d13.4732306
X-RAY DIFFRACTIONf_chiral_restr0.036980
X-RAY DIFFRACTIONf_plane_restr0.0041065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.54-3.760.36431040.30081823X-RAY DIFFRACTION63
3.76-4.050.31271430.27482943X-RAY DIFFRACTION100
4.05-4.460.2611510.22262976X-RAY DIFFRACTION100
4.46-5.10.25521550.21962983X-RAY DIFFRACTION100
5.1-6.420.32871490.273036X-RAY DIFFRACTION100
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)
14.7507-1.8086-1.86136.6714.21037.7119-0.52611.42750.0455-1.8605-0.55861.247-0.47170.47961.03731.4642-0.2199-0.15911.16910.04090.8583-2.760136.081629.9557
22.5073-0.5794.04421.05130.0637.9567-0.40270.63490.3608-0.33810.14710.3772-0.49930.76490.28011.2227-0.29920.16530.96740.14021.055214.354635.499164.907
38.97095.34212.57834.39313.74787.35030.249-1.0248-0.2254-0.9568-0.34910.3808-0.4676-0.1385-0.12260.83190.05290.19910.84030.05510.642235.524844.11394.9437
44.57762.35586.30495.09163.01638.73870.0611.4745-0.9129-0.86910.6293-0.6710.67240.9877-0.51790.83740.01820.05271.0306-0.17060.829955.948455.7049101.1153
55.83442.1853.03055.24683.833.1744-1.4275-0.5750.37661.1161-0.3424-0.72712.29091.33731.80892.12960.4399-0.07471.05870.06630.99921.801134.937634.474
68.35472.3125-4.8982.4903-4.62378.6436-1.22930.58942.8146-2.2361-0.28373.4363-1.8819-2.75481.69181.9880.5143-1.12771.3724-0.38891.3698-10.767939.936351.3736
79.67355.24245.3986.91937.87429.5629-0.02261.2023-1.264-0.2021.48040.1163-4.251-0.2177-0.92441.29870.0682-0.11911.21210.57731.244-5.312952.188244.8207
82.81821.81151.44252.17141.78494.0402-0.29190.34810.10010.4320.34860.0909-0.36420.66580.02571.12530.04350.07891.0331-0.00670.807933.76356.136486.1991
98.0842-0.4466-0.00673.4743.11166.0902-0.2298-0.16820.5073-0.0640.1602-0.3884-0.42131.0860.070.8427-0.1409-0.00671.09560.05350.76470.776566.469388.5525
104.73455.1774-0.0017.3573-0.44680.7736-0.3797-0.0984-0.6843-0.66710.2242-0.58460.12230.2110.14240.96240.12790.1410.897-0.07920.705545.760438.040283.3031
115.2588-3.4182.93395.2314-0.883.9426-0.29550.28170.1678-0.6988-0.07520.3038-0.2594-0.46460.31311.0816-0.1828-0.04960.6998-0.01630.69388.961525.839877.5257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 529 through 566 )
2X-RAY DIFFRACTION2chain 'B' and (resid 567 through 673 )
3X-RAY DIFFRACTION3chain 'B' and (resid 674 through 706 )
4X-RAY DIFFRACTION4chain 'B' and (resid 707 through 722 )
5X-RAY DIFFRACTION5chain 'C' and (resid 531 through 557 )
6X-RAY DIFFRACTION6chain 'C' and (resid 558 through 568 )
7X-RAY DIFFRACTION7chain 'C' and (resid 569 through 595 )
8X-RAY DIFFRACTION8chain 'C' and (resid 596 through 624 )
9X-RAY DIFFRACTION9chain 'G' and (resid 123 through 296 )
10X-RAY DIFFRACTION10chain 'G' and (resid 297 through 466 )
11X-RAY DIFFRACTION11chain 'G' and (resid 467 through 679 )

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