6FGZ

Cyanidioschyzon merolae Dnm1 (CmDnm1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.411 
  • R-Value Work: 0.344 
  • R-Value Observed: 0.351 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of a mitochondrial fission dynamin in the closed conformation.

Bohuszewicz, O.Low, H.H.

(2018) Nat Struct Mol Biol 25: 722-731

  • DOI: 10.1038/s41594-018-0097-6
  • Primary Citation of Related Structures:  
    6FGZ

  • PubMed Abstract: 
  • Dynamin 1-like proteins (DNM1-L) are mechanochemical GTPases that induce membrane fission in mitochondria and peroxisomes. Their mechanism depends on conformational changes driven by nucleotide and lipid cycling. Here we show the crystal structure of a mitochondrial fission dynamin (CmDnm1) from the algae Cyanidioschyzon merolae ...

    Dynamin 1-like proteins (DNM1-L) are mechanochemical GTPases that induce membrane fission in mitochondria and peroxisomes. Their mechanism depends on conformational changes driven by nucleotide and lipid cycling. Here we show the crystal structure of a mitochondrial fission dynamin (CmDnm1) from the algae Cyanidioschyzon merolae. Unlike other eukaryotic dynamin structures, CmDnm1 is in a hinge 1 closed conformation, with the GTPase domain compacted against the stalk. Within the crystal, CmDnm1 packs as a diamond-shaped tetramer that is consistent with an inactive off-membrane state. Crosslinking, photoinduced electron transfer assays, and electron microscopy verify these structures. In vitro, CmDnm1 forms concentration-dependent rings and protein-lipid tubes reminiscent of DNM1-L and classical dynamin with hinge 1 open. Our data provides a mechanism for filament collapse and membrane release that may extend to other dynamin family members. Additionally, hinge 1 closing may represent a key conformational change that contributes to membrane fission.


    Organizational Affiliation

    Department of Life Sciences, Imperial College, London, UK. h.low@imperial.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DynaminA774Cyanidioschyzon merolaeMutation(s): 0 
Gene Names: Dnm1
UniProt
Find proteins for Q84Y91 (Cyanidioschyzon merolae)
Explore Q84Y91 
Go to UniProtKB:  Q84Y91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84Y91
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.00 Å
  • R-Value Free: 0.411 
  • R-Value Work: 0.344 
  • R-Value Observed: 0.351 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.219α = 90
b = 188.219β = 90
c = 163.627γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOSFLMdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom097328/Z/11/Z

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release