4W8F

Crystal structure of the dynein motor domain in the AMPPNP-bound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.541 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Allosteric communication in the Dynein motor domain.

Bhabha, G.Cheng, H.C.Zhang, N.Moeller, A.Liao, M.Speir, J.A.Cheng, Y.Vale, R.D.

(2014) Cell 159: 857-868

  • DOI: 10.1016/j.cell.2014.10.018

  • PubMed Abstract: 
  • Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which collectively provide insight into the roles of dyn ...

    Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which collectively provide insight into the roles of dynein's two major ATPase sites, AAA1 and AAA3, in the conformational change mechanism. ATP binding to AAA1 triggers a cascade of conformational changes that propagate to all six AAA domains and cause a large movement of the "linker," dynein's mechanical element. In contrast to the role of AAA1 in driving motility, nucleotide transitions in AAA3 gate the transmission of conformational changes between AAA1 and the linker, suggesting that AAA3 acts as a regulatory switch. Further structural and mutational studies also uncover a role for the linker in regulating the catalytic cycle of AAA1. Together, these results reveal how dynein's two major ATP-binding sites initiate and modulate conformational changes in the motor domain during motility.


    Organizational Affiliation

    Howard Hughes Medical Institute and the Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynein heavy chain lysozyme chimera
A, B
2661Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Enterobacteria phage T4
This entity is chimeric
Mutation(s): 1 
Gene Names: DYN1 (DHC1), E
EC: 3.2.1.17
Find proteins for P36022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36022
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.541 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 137.730α = 90.00
b = 154.380β = 96.59
c = 177.550γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM09731

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary