X-ray structure of an MTBD truncation mutant of dynein motor domain

Experimental Data Snapshot

  • Resolution: 2.81 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 

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This is version 1.3 of the entry. See complete history


The 2.8 A crystal structure of the dynein motor domain

Kon, T.Oyama, T.Shimo-Kon, R.Imamula, K.Shima, T.Sutoh, K.Kurisu, G.

(2012) Nature 484: 345-350

  • DOI: https://doi.org/10.1038/nature10955
  • Primary Citation of Related Structures:  
    3VKG, 3VKH

  • PubMed Abstract: 

    Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport. Here we report the most complete structure obtained so far, to our knowledge, of the 380-kDa motor domain of Dictyostelium discoideum cytoplasmic dynein at 2.8 Å resolution; the data are reliable enough to discuss the structure and mechanism at the level of individual amino acid residues. Features that can be clearly visualized at this resolution include the coordination of ADP in each of four distinct nucleotide-binding sites in the ring-shaped AAA(+) ATPase unit, a newly identified interaction interface between the ring and mechanical linker, and junctional structures between the ring and microtubule-binding stalk, all of which should be critical for the mechanism of dynein motility. We also identify a long-range allosteric communication pathway between the primary ATPase and the microtubule-binding sites. Our work provides a framework for understanding the mechanism of dynein-based motility.

  • Organizational Affiliation

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan. takahide.kon@protein.osaka-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynein heavy chain, cytoplasmic
A, B
3,245Dictyostelium discoideumMutation(s): 0 
Gene Names: DDB_G0276355dhcAslime mold
Find proteins for P34036 (Dictyostelium discoideum)
Explore P34036 
Go to UniProtKB:  P34036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34036
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
J [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B]
C10 H15 N5 O10 P2
Query on SPM

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
N [auth B],
O [auth B]
C10 H26 N4
Query on MG

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B],
Q [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.81 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.256α = 90
b = 221.806β = 90
c = 192.898γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references, Structure summary
  • Version 1.2: 2017-06-07
    Changes: Source and taxonomy
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations