2AKA

Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin 1 from Rattus norvegicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the GTPase domain of rat dynamin 1.

Reubold, T.F.Eschenburg, S.Becker, A.Leonard, M.Schmid, S.L.Vallee, R.B.Kull, F.J.Manstein, D.J.

(2005) Proc Natl Acad Sci U S A 102: 13093-13098

  • DOI: 10.1073/pnas.0506491102
  • Primary Citation of Related Structures:  
    2AKA

  • PubMed Abstract: 
  • Here, we present the 1.9-A crystal structure of the nucleotide-free GTPase domain of dynamin 1 from Rattus norvegicus. The structure corresponds to an extended form of the canonical GTPase fold observed in Ras proteins. Both nucleotide-binding switch motifs are well resolved, adopting conformations that closely resemble a GTP-bound state not previously observed for nucleotide-free GTPases ...

    Here, we present the 1.9-A crystal structure of the nucleotide-free GTPase domain of dynamin 1 from Rattus norvegicus. The structure corresponds to an extended form of the canonical GTPase fold observed in Ras proteins. Both nucleotide-binding switch motifs are well resolved, adopting conformations that closely resemble a GTP-bound state not previously observed for nucleotide-free GTPases. Two highly conserved arginines, Arg-66 and Arg-67, greatly restrict the mobility of switch I and are ideally positioned to relay information about the nucleotide state to other parts of the protein. Our results support a model in which switch I residue Arg-59 gates GTP binding in an assembly-dependent manner and the GTPase effector domain functions as an assembly-dependent GTPase activating protein in the fashion of RGS-type GAPs.


    Related Citations: 
    • A structural model for actin-induced nucleotide release in myosin
      Reubold, T.F., Eschenburg, S., Becker, A., Kull, F.J., Manstein, D.J.
      (2003) Nat Struct Mol Biol 10: 826

    Organizational Affiliation

    Abteilung Biophysik, Max-Planck-Institut für Medizinische Forschung, Jahnstrasse 29, D-69120 Heidelberg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
myosin II heavy chainA776Dictyostelium discoideumMutation(s): 0 
Gene Names: mhcADDB_G0286355
Find proteins for P08799 (Dictyostelium discoideum)
Explore P08799 
Go to UniProtKB:  P08799
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
LINKERB [auth L]13N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Dynamin-1C [auth B]299Rattus norvegicusMutation(s): 0 
Gene Names: Dnm1Dnm
EC: 3.6.5.5
Find proteins for P21575 (Rattus norvegicus)
Explore P21575 
Go to UniProtKB:  P21575
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.42α = 90
b = 126.99β = 90
c = 160.81γ = 90
Software Package:
Software NamePurpose
CAD4data collection
XDSdata reduction
CNSrefinement
CAD4data reduction
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance