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- PDB-9w9h: Cryo-EM structure of the mouse kinesin-2 tail in complex with KAP... -

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Basic information

Entry
Database: PDB / ID: 9w9h
TitleCryo-EM structure of the mouse kinesin-2 tail in complex with KAP3 adaptor
Components
  • Kinesin-associated protein 3
  • Kinesin-like protein KIF3A
  • Kinesin-like protein KIF3B
KeywordsMOTOR PROTEIN / Kinesin-2 motor Intracellular transport Kinesin-adaptor complex
Function / homology
Function and homology information


positive regulation of calcium-dependent cell-cell adhesion / opsin transport / epidermal stem cell homeostasis / kinesin II complex / anterograde dendritic transport / intraciliary transport particle B binding / periciliary membrane compartment / Activation of SMO / Intraflagellar transport / centriole-centriole cohesion ...positive regulation of calcium-dependent cell-cell adhesion / opsin transport / epidermal stem cell homeostasis / kinesin II complex / anterograde dendritic transport / intraciliary transport particle B binding / periciliary membrane compartment / Activation of SMO / Intraflagellar transport / centriole-centriole cohesion / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of keratinocyte proliferation / microtubule anchoring at centrosome / Kinesins / intraciliary transport / cilium movement / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / COPI-dependent Golgi-to-ER retrograde traffic / motile cilium assembly / Hedgehog 'off' state / dorsal/ventral neural tube patterning / dentate gyrus development / MHC class II antigen presentation / non-motile cilium assembly / negative regulation of thymocyte apoptotic process / dorsal/ventral pattern formation / determination of left/right symmetry / microtubule motor activity / anterior/posterior pattern specification / neural precursor cell proliferation / neural tube development / negative regulation of cardiac muscle cell apoptotic process / motile cilium / negative regulation of neuroblast proliferation / smoothened signaling pathway / spectrin binding / thymocyte apoptotic process / positive regulation of cytokinesis / heart looping / forebrain development / keratinocyte proliferation / axoneme / cilium assembly / neuroblast proliferation / mitotic spindle assembly / kinesin binding / epidermis development / photoreceptor outer segment / microtubule-based process / vesicle-mediated transport / cardiac muscle cell apoptotic process / photoreceptor inner segment / centriole / dendrite cytoplasm / positive regulation of epithelial cell proliferation / condensed nuclear chromosome / spindle microtubule / kidney development / small GTPase binding / intracellular protein localization / heart development / microtubule cytoskeleton / midbody / protein phosphatase binding / microtubule binding / dendritic spine / in utero embryonic development / microtubule / cell population proliferation / postsynapse / neuron projection / cilium / ciliary basal body / axon / apoptotic process / dendrite / centrosome / negative regulation of apoptotic process / glutamatergic synapse / endoplasmic reticulum / Golgi apparatus / ATP binding / cytosol
Similarity search - Function
Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Kinesin-like protein / Armadillo/plakoglobin ARM repeat profile. / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. ...Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Kinesin-like protein / Armadillo/plakoglobin ARM repeat profile. / 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-like protein KIF3A / Kinesin-associated protein 3 / Kinesin-like protein KIF3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsJiang, X. / Danev, R. / Yanagisawa, H. / Kikkawa, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER2202 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05247 Japan
Japan Society for the Promotion of Science (JSPS)JP24KF0141 Japan
Japan Society for the Promotion of Science (JSPS)JP24K18106 Japan
CitationJournal: Sci Adv / Year: 2025
Title: The hook-like adaptor and cargo-binding (HAC) domain in the kinesin-2 tail enables adaptor assembly and cargo recognition.
Authors: Xuguang Jiang / Radostin Danev / Sotaro Ichinose / Baichun Niu / Sumio Ohtsuki / Haruaki Yanagisawa / Satoru Nagatoishi / Kouhei Tsumoto / Nobutaka Hirokawa / Masahide Kikkawa /
Abstract: Intracellular transport relies on motor proteins such as kinesins to deliver cargo along microtubules, yet how they recognize cargo remains unclear. Here, we present high-resolution cryo-electron ...Intracellular transport relies on motor proteins such as kinesins to deliver cargo along microtubules, yet how they recognize cargo remains unclear. Here, we present high-resolution cryo-electron microscopy structures of the heterotrimeric kinesin-2 complex (KIF3A/KIF3B/KAP3) bound to the cargo protein APC. Our findings reveal a previously uncharacterized KIF3 tail hook-like motif, termed the "HAC" domain, which mediates binding to both KAP3 adaptor and APC cargo. Within this domain, the KIF3A helical regions ensure cargo specificity, while a β-hairpin and KIF3B provide structural support. Biochemical and neuronal experiments confirm its functional importance. Notably, the HAC/KAP3 structure resembles hook-like architectures seen in kinesin-1 and dynein, suggesting a shared cargo recognition framework. These findings also shed light on kinesin-2 cargo specificity and offer a structural framework for understanding related neuronal transport mechanisms.
History
DepositionAug 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinesin-like protein KIF3A
B: Kinesin-like protein KIF3B
C: Kinesin-associated protein 3


Theoretical massNumber of molelcules
Total (without water)139,7883
Polymers139,7883
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, SEC-MALS, SEC-SAXS
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Kinesin-like protein KIF3A / Microtubule plus end-directed kinesin motor 3A


Mass: 27706.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Clone in pETDuet-1 MCS1 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif3a, Kif3 / Plasmid: pETDuet-1 MCS2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P28741
#2: Protein Kinesin-like protein KIF3B / Microtubule plus end-directed kinesin motor 3B


Mass: 31857.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Clone in pETDuet-1 MCS2 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif3b / Plasmid: pETDuet-1 MCS2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q61771
#3: Protein Kinesin-associated protein 3 / KAP-3 / KAP3


Mass: 80224.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kifap3 / Plasmid: pETDuet-1 MCS2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P70188
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of kinesin-2 KIF3A/B and KAP3 adaptor / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.145 MDa / Experimental value: YES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pETDuet-1 for KIF3A/B, pET21b for KAP3
Buffer solutionpH: 8
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Cs: 1.55 mm / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 65.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 34176
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9701817
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 539244 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: ModelAngelo de novo model / Source name: Other / Type: other

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