9W9I | pdb_00009w9i

Cryo-EM structure of the kinesin-2 tail domain in complex with KAP3 and APC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The hook-like adaptor and cargo-binding (HAC) domain in the kinesin-2 tail enables adaptor assembly and cargo recognition.

Jiang, X.Danev, R.Ichinose, S.Niu, B.Ohtsuki, S.Yanagisawa, H.Nagatoishi, S.Tsumoto, K.Hirokawa, N.Kikkawa, M.

(2025) Sci Adv 11: eady5861-eady5861

  • DOI: https://doi.org/10.1126/sciadv.ady5861
  • Primary Citation of Related Structures:  
    9W9H, 9W9I

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF3A178Mus musculusMutation(s): 0 
Gene Names: Kif3aKif3
UniProt
Find proteins for P28741 (Mus musculus)
Explore P28741 
Go to UniProtKB:  P28741
Entity Groups  
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UniProt GroupP28741
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF3B, N-terminally processed220Mus musculusMutation(s): 0 
Gene Names: Kif3b
UniProt & NIH Common Fund Data Resources
Find proteins for Q61771 (Mus musculus)
Explore Q61771 
Go to UniProtKB:  Q61771
IMPC:  MGI:107688
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61771
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-associated protein 3693Mus musculusMutation(s): 0 
Gene Names: Kifap3
UniProt & NIH Common Fund Data Resources
Find proteins for P70188 (Mus musculus)
Explore P70188 
Go to UniProtKB:  P70188
IMPC:  MGI:107566
Entity Groups  
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UniProt GroupP70188
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Adenomatous polyposis coli protein680Mus musculusMutation(s): 0 
Gene Names: Apc
UniProt
Find proteins for Q61315 (Mus musculus)
Explore Q61315 
Go to UniProtKB:  Q61315
Entity Groups  
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UniProt GroupQ61315
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJER2202
Japan Society for the Promotion of Science (JSPS)JapanJP21H05247
Japan Society for the Promotion of Science (JSPS)JapanJP24KF0141
Japan Society for the Promotion of Science (JSPS)JapanJP24K18106

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Data collection, Database references