3VKG

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

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: 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 ...

    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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dynein heavy chain, cytoplasmicA, B3245Dictyostelium discoideumMutation(s): 0 
Gene Names: DDB_G0276355, dhcA, slime mold
UniProt
Find proteins for P34036 (Dictyostelium discoideum)
Explore P34036 
Go to UniProtKB:  P34036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34036
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
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]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
SPM
Query on SPM
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
N [auth B],
O [auth B]		SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
I [auth A],
P [auth B],
Q [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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