3VKG | pdb_00003vkg

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 (Depositor), 0.319 (DCC) 
  • R-Value Work: 
    0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3VKG

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/nature10955
  • Primary Citation 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

Macromolecule Content 

  • Total Structure Weight: 745.15 kDa 
  • Atom Count: 45,284 
  • Modeled Residue Count: 5,807 
  • Deposited Residue Count: 6,490 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dynein heavy chain, cytoplasmic
A, B
3,245Dictyostelium discoideumMutation(s): 0 
Gene Names: DDB_G0276355dhcAslime 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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / 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
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
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
P [auth B],
Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free:  0.319 (Depositor), 0.319 (DCC) 
  • R-Value Work:  0.262 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
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

View Full Validation Report



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