8I3J

Crystal structure of human inner-arm dynein heavy chain d stalk and microtubule binding domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the stalk region of axonemal inner-arm dynein-d reveals unique features in the coiled-coil and microtubule-binding domain.

Ko, S.Toda, A.Tanaka, H.Yu, J.Kurisu, G.

(2023) FEBS Lett 597: 2149-2160

  • DOI: https://doi.org/10.1002/1873-3468.14690
  • Primary Citation of Related Structures:  
    8I3J

  • PubMed Abstract: 

    Axonemal dynein is an ATP-dependent microtubular motor protein responsible for cilia and flagella beating, and its dysfunction can cause diseases such as primary ciliary dyskinesia and sperm dysmotility. Despite its biological importance, structure-based mechanisms underlying axonemal dynein motors remain unclear. Here, we determined the X-ray crystal structure of the human inner-arm dynein-d (DNAH1) stalk region, which contains a long antiparallel coiled-coil and a microtubule-binding domain (MTBD), at 2.7 Å resolution. Notably, differences in the relative orientation of the coiled-coil and MTBD in comparison with other dyneins, as well as the diverse orientations of the MTBD flap region among various isoforms, lead us to propose a 'spike shoe model' with an altered stepping angle for the interaction between IAD-d and microtubules. Based on these findings, we discuss isoform-specific functions of the axonemal dynein stalk MTBDs.


  • Organizational Affiliation

    Protein Crystallography Laboratory, Institute for Protein Research, Osaka University, Suita, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein axonemal heavy chain 1277Homo sapiensMutation(s): 0 
Gene Names: DNAH1DHC7DNAHC1KIAA1410
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2D7 (Homo sapiens)
Explore Q9P2D7 
Go to UniProtKB:  Q9P2D7
PHAROS:  Q9P2D7
GTEx:  ENSG00000114841 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2D7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.258 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.468α = 90
b = 147.468β = 90
c = 85.075γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
SHELXCDphasing
AutoSolphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18H02390

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-09-27
    Changes: Database references
  • Version 1.3: 2023-11-15
    Changes: Data collection