8I3J | pdb_00008i3j

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 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 31.49 kDa 
  • Atom Count: 2,172 
  • Modeled Residue Count: 277 
  • Deposited Residue Count: 277 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
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

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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
  • Version 1.4: 2024-10-09
    Changes: Structure summary