9KNS | pdb_00009kns

Crystal structure of Hook3(553-624)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for assembly and activation of the Hook3 - KIF1C complex-dependent transport machinery.

Lee, H.S.Yu, D.Baek, K.E.Shin, H.C.Kim, S.J.Do Heo, W.Ku, B.

(2025) EMBO Rep 26: 2945-2966

  • DOI: https://doi.org/10.1038/s44319-025-00458-w
  • Primary Citation of Related Structures:  
    9KNS, 9KO8

  • PubMed Abstract: 

    Microtubule-associated cargo transport, a central process governing the localization and movement of various cellular cargoes, is orchestrated by the coordination of two types of motor proteins (kinesins and dyneins), along with diverse adaptor and accessory proteins. Hook microtubule tethering protein 3 (Hook3) is a cargo adaptor that serves as a scaffold for recruiting kinesin family member 1C (KIF1C) and dynein, thereby regulating bidirectional cargo transport. Herein, we conduct structural and functional analyses of how Hook3 mediates KIF1C-dependent anterograde cargo transport through interaction with KIF1C and PTPN21. We verify the interactions among the three proteins and determine the crystal structure of the Hook3(553-624) - KIF1C(714-809) complex. Subsequent structure-based mutational analysis demonstrates that this complex formation is necessary and sufficient for the interaction between the full-length proteins in HEK293T cells and plays a key role in Hook3- and KIF1C-mediated anterograde transport in RPE1 cells. Thus, this study provides a basis for a comprehensive understanding of how Hook3 cooperates with other components during the initial steps of activation and assembly of the Hook3- and KIF1C-dependent cargo transport machinery.


  • Organizational Affiliation
    • Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Hook homolog 3
A, B
75Homo sapiensMutation(s): 0 
Gene Names: HOOK3
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VS8 (Homo sapiens)
Explore Q86VS8 
Go to UniProtKB:  Q86VS8
PHAROS:  Q86VS8
GTEx:  ENSG00000168172 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86VS8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.747α = 90
b = 78.747β = 90
c = 180.036γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfKGM9952421
Other governmentKorea, Republic OfCRC22021-700

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Database references
  • Version 1.2: 2025-06-18
    Changes: Database references