9IKB | pdb_00009ikb

Crystal structure of heterotrimeric Kinesin-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free: 
    0.271 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

A mutual co-recognition mechanism ensures the proper assembly of heterotrimeric kinesin-2 for intraflagellar transport.

Ren, J.Zhao, L.Chen, G.Ou, G.Feng, W.

(2025) Nat Commun 16: 6816-6816

  • DOI: https://doi.org/10.1038/s41467-025-62152-8
  • Primary Citation of Related Structures:  
    9IKB

  • PubMed Abstract: 

    Heterotrimeric kinesin-2, composed of two distinct kinesin motors and a kinesin-associated protein (KAP), is essential for intraflagellar transport and ciliogenesis. KAP specifically recognizes the hetero-paired motor tails for the holoenzyme assembly, but the underlying mechanism remains unclear. Here, we determine the structure of KAP-1 in complex with the hetero-paired tails from kinesin-2 motors KLP-20 and KLP-11. KAP-1 forms an elongated superhelical structure characterized by a central groove and a C-terminal helical (CTH)-hook. The two motor tails fold together and are co-recognized by the central groove of KAP-1. The adjacent hetero-pairing trigger sequences preceding the two tails form an intertwined heterodimer, which co-captures the CTH-hook of KAP-1 to complete the holoenzyme assembly. Mutations in the interfaces between KAP-1 and the two tails disrupt the heterotrimeric kinesin-2 complex and impair kinesin-2-mediated intraflagellar transport. Thus, KAP-1 and the hetero-paired motors are mutually co-recognized, ensuring the proper assembly of heterotrimeric kinesin-2 for cargo transport.


  • Organizational Affiliation
    • State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like proteinA [auth B]254Caenorhabditis elegansMutation(s): 0 
Gene Names: klp-11CELE_F20C5.2F20C5.2
UniProt
Find proteins for Q19633 (Caenorhabditis elegans)
Explore Q19633 
Go to UniProtKB:  Q19633
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UniProt GroupQ19633
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein klp-20B [auth C]120Caenorhabditis elegansMutation(s): 0 
Gene Names: klp-20Y50D7A.6
UniProt
Find proteins for Q965T6 (Caenorhabditis elegans)
Explore Q965T6 
Go to UniProtKB:  Q965T6
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UniProt GroupQ965T6
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-associated proteinC [auth G]589Caenorhabditis elegansMutation(s): 0 
Gene Names: kap-1CELE_F08F8.3F08F8.3
UniProt
Find proteins for G5EEE6 (Caenorhabditis elegans)
Explore G5EEE6 
Go to UniProtKB:  G5EEE6
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UniProt GroupG5EEE6
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.54 Å
  • R-Value Free:  0.271 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.445α = 90
b = 107.445β = 90
c = 255.397γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31971160,5242021

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references