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- PDB-9w9i: Cryo-EM structure of the kinesin-2 tail domain in complex with KA... -

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Basic information

Entry
Database: PDB / ID: 9w9i
TitleCryo-EM structure of the kinesin-2 tail domain in complex with KAP3 and APC
Components
  • Adenomatous polyposis coli protein
  • Kinesin-associated protein 3
  • Kinesin-like protein KIF3A
  • Kinesin-like protein KIF3B, N-terminally processed
KeywordsMOTOR PROTEIN / Kinesin-2 motor Intracellular transport Kinesin-adaptor-cargo complex
Function / homology
Function and homology information


negative regulation of odontogenesis / axis specification / positive regulation of calcium-dependent cell-cell adhesion / kinesin II complex / opsin transport / negative regulation of epithelial cell proliferation involved in prostate gland development / intraciliary transport particle B binding / isoflavonoid biosynthetic process / Apoptotic cleavage of cellular proteins / periciliary membrane compartment ...negative regulation of odontogenesis / axis specification / positive regulation of calcium-dependent cell-cell adhesion / kinesin II complex / opsin transport / negative regulation of epithelial cell proliferation involved in prostate gland development / intraciliary transport particle B binding / isoflavonoid biosynthetic process / Apoptotic cleavage of cellular proteins / periciliary membrane compartment / Beta-catenin phosphorylation cascade / proximal/distal pattern formation / Intraflagellar transport / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nitrogen cycle metabolic process / regulation of epithelial cell differentiation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / Deactivation of the beta-catenin transactivating complex / intraciliary transport / Ovarian tumor domain proteases / anterograde dendritic transport of neurotransmitter receptor complex / Kinesins / negative regulation of cell cycle G1/S phase transition / : / Scrib-APC-beta-catenin complex / negative regulation of cardiac muscle cell proliferation / COPI-dependent Golgi-to-ER retrograde traffic / photoreceptor connecting cilium / Degradation of beta-catenin by the destruction complex / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / cell body fiber / cilium organization / metaphase/anaphase transition of mitotic cell cycle / pattern specification process / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / cell projection membrane / regulation of osteoclast differentiation / negative regulation of microtubule depolymerization / anterior/posterior pattern specification / MHC class II antigen presentation / S-adenosylmethionine-dependent methyltransferase activity / beta-catenin destruction complex / dorsal/ventral pattern formation / catenin complex / microtubule plus-end binding / cell fate specification / protein kinase regulator activity / O-methyltransferase activity / muscle cell cellular homeostasis / regulation of microtubule-based process / protein-containing complex localization / skin development / microtubule motor activity / kinesin complex / somatic stem cell population maintenance / stem cell population maintenance / negative regulation of G1/S transition of mitotic cell cycle / ciliary transition zone / microtubule-based movement / mitotic spindle assembly checkpoint signaling / regulation of osteoblast differentiation / hair follicle development / positive regulation of cytokinesis / neuron projection terminus / retina development in camera-type eye / canonical Wnt signaling pathway / establishment or maintenance of cell polarity / regulation of cell differentiation / mitotic cytokinesis / positive regulation of cell division / negative regulation of Wnt signaling pathway / dynein complex binding / mitotic spindle assembly / lateral plasma membrane / chromosome organization / bicellular tight junction / cilium assembly / axoneme / photoreceptor outer segment / kinesin binding / axonal growth cone / thymus development / microtubule-based process / positive regulation of microtubule polymerization / negative regulation of MAPK cascade / kidney development / axonogenesis / vesicle-mediated transport / cell projection / cytoplasmic microtubule organization / photoreceptor inner segment / regulation of cell migration / positive regulation of cell adhesion / dendrite cytoplasm / condensed nuclear chromosome / spindle microtubule / adherens junction / positive regulation of cell differentiation
Similarity search - Function
Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein ...Kinesin-associated protein 3 / Kinesin-associated protein (KAP) / Kinesin-associated protein (KAP) / Adenomatous polyposis coli protein repeat / SAMP / EB-1 binding / Adenomatous polyposis coli protein basic domain / Adenomatous polyposis coli protein, 15 residue repeat / Adenomatous polyposis coli (APC) family / Adenomatous polyposis coli protein / Adenomatous polyposis coli, N-terminal dimerisation domain / APC, N-terminal coiled-coil domain superfamily / Adenomatous polyposis coli (APC) repeat / APC repeat / SAMP Motif / EB-1 Binding Domain / APC basic domain / APC 15 residue motif / Adenomatous polyposis coli tumour suppressor protein / Armadillo-associated region on APC / Unstructured region on APC between 1st and 2nd catenin-bdg motifs / Unstructured region on APC between 1st two creatine-rich regions / Unstructured region on APC between APC_crr and SAMP / Unstructured region on APC between SAMP and APC_crr / Unstructured region on APC between APC_crr regions 5 and 6 / Coiled-coil N-terminus of APC, dimerisation domain / Adenomatous polyposis coli (APC) repeat / Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Kinesin-like protein / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Coniferyl alcohol 9-O-methyltransferase / Kinesin-associated protein 3 / Adenomatous polyposis coli protein / Kinesin-like protein KIF3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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: 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
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF3A
B: Kinesin-like protein KIF3B, N-terminally processed
C: Kinesin-associated protein 3
D: Adenomatous polyposis coli protein


Theoretical massNumber of molelcules
Total (without water)202,1664
Polymers202,1664
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 21084.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif3a, Kif3 / Production host: Escherichia coli (E. coli) / References: UniProt: P28741
#2: Protein Kinesin-like protein KIF3B, N-terminally processed


Mass: 25440.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif3b / Production host: Escherichia coli (E. coli) / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P70188
#4: Protein Adenomatous polyposis coli protein / Protein APC / mAPC


Mass: 75417.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Apc / Production host: Escherichia coli (E. coli) / References: UniProt: Q61315
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: Tetrameric complex of kinesin-2 KIF3A/B/KAP3 and cargo APC
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: NO
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.: 0.0375 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid 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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Alignment procedure: BASIC / C2 aperture diameter: 50 µm / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Specimen-ID: 1

IDAccelerating voltage (kV)ModelCs (mm)Nominal defocus max (nm)Nominal defocus min (nm)Nominal magnification (X)
1200JEOL CRYO ARM 2001.55180060080000
2300TFS KRIOS2.716001000130000
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real imagesDetails (eV)
1164.7GATAN K3 (6k x 4k)136020
2263GATAN K3 (6k x 4k)119918tilted-stage image collection with tilt angles of 30 and 40 degrees
EM imaging optics
IDImaging-IDEnergyfilter slit width (eV)
1120
2220
Image scans
WidthHeightIDImage recording-IDEntry-ID
57604092119W9I
57604092229W9I

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Processing

EM software
IDNameCategoryImaging-ID
1cryoSPARCparticle selection
2SerialEMimage acquisition1
4cryoSPARCCTF correction
7PHENIXmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIXmodel refinement
15Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 12833027
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 407310 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: Initial local fitting was done using Phenix dock-in-map tool.
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetails (eV)Initial refinement model-ID
19W9H

9w9h

9W9Hchains, A-C1
24YJE

4yje

4YJEchain D2

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