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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 / canonical Wnt signaling pathway involved in negative regulation of apoptotic process / canonical Wnt signaling pathway involved in positive regulation of apoptotic process / negative regulation of acinar cell proliferation / axis specification / positive regulation of calcium-dependent cell-cell adhesion / opsin transport / epidermal stem cell homeostasis / kinesin II complex / anterograde dendritic transport ...negative regulation of odontogenesis / canonical Wnt signaling pathway involved in negative regulation of apoptotic process / canonical Wnt signaling pathway involved in positive regulation of apoptotic process / negative regulation of acinar cell proliferation / axis specification / 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 / Apoptotic cleavage of cellular proteins / periciliary membrane compartment / acinar cell proliferation / Activation of SMO / Beta-catenin phosphorylation cascade / Intraflagellar transport / Disassembly of the destruction complex and recruitment of AXIN to the membrane / nitrogen cycle metabolic process / centriole-centriole cohesion / Deactivation of the beta-catenin transactivating complex / Ovarian tumor domain proteases / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of keratinocyte proliferation / regulation of epithelial cell differentiation / Kinesins / microtubule anchoring at centrosome / negative regulation of cell cycle G1/S phase transition / intraciliary transport / Degradation of beta-catenin by the destruction complex / cilium movement / Scrib-APC-beta-catenin complex / photoreceptor connecting cilium / inner ear receptor cell stereocilium organization / COPI-dependent Golgi-to-ER retrograde traffic / motile cilium assembly / proximal/distal pattern formation / negative regulation of epithelial cell proliferation involved in prostate gland development / positive regulation of fibroblast apoptotic process / regulation of epithelial cell migration / negative regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of attachment of spindle microtubules to kinetochore / Hedgehog 'off' state / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / metaphase/anaphase transition of mitotic cell cycle / dorsal/ventral neural tube patterning / cell projection membrane / regulation of osteoclast differentiation / pattern specification process / negative regulation of epithelial cell apoptotic process / dentate gyrus development / fibroblast migration / negative regulation of microtubule depolymerization / epithelial cell proliferation involved in prostate gland development / MHC class II antigen presentation / beta-catenin destruction complex / microtubule plus-end binding / protein kinase regulator activity / non-motile cilium assembly / negative regulation of thymocyte apoptotic process / dorsal/ventral pattern formation / endothelial cell proliferation / regulation of microtubule-based process / determination of left/right symmetry / fibroblast apoptotic process / microtubule depolymerization / odontogenesis / epithelial cell apoptotic process / microtubule motor activity / positive regulation of fibroblast migration / 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 / regulation of osteoblast differentiation / skin development / spectrin binding / muscle cell cellular homeostasis / thymocyte apoptotic process / stem cell population maintenance / mitotic spindle assembly checkpoint signaling / positive regulation of cytokinesis / heart looping / negative regulation of endothelial cell proliferation / forebrain development / negative regulation of Wnt signaling pathway / microtubule polymerization / dynein complex binding / regulation of cell differentiation / mitotic cytokinesis / positive regulation of cell division / keratinocyte proliferation / lateral plasma membrane / axoneme / somatic stem cell population maintenance / cilium assembly
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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF3A / 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
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 codeDetailsInitial refinement model-ID
19W9H

9w9h

9W9Hchains, A-C1
24YJE

4yje

4YJEchain D2

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