6FGZ | pdb_00006fgz

Cyanidioschyzon merolae Dnm1 (CmDnm1)

• PDB DOI: https://doi.org/10.2210/pdb6FGZ/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Cyanidioschyzon merolae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-01-11 Released: 2018-08-15 
• Deposition Author(s): Bohuszewicz, O., Low, H.H.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Free: 
  0.411 (Depositor), 0.420 (DCC) 
• R-Value Work: 
  0.344 (Depositor), 0.350 (DCC) 
• R-Value Observed: 
  0.351 (Depositor) 

Starting Model: experimental

Literature

Structure of a mitochondrial fission dynamin in the closed conformation.

Bohuszewicz, O., Low, H.H.

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

• PubMed: 30061604 
• DOI: https://doi.org/10.1038/s41594-018-0097-6
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Life Sciences, Imperial College, London, UK.
Department of Life Sciences, Imperial College, London, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.29 kDa 
• Atom Count: 2,606 
• Modeled Residue Count: 526 
• Deposited Residue Count: 774 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynamin	A	774	Cyanidioschyzon merolae	Mutation(s): 0  Gene Names: Dnm1
UniProt
Find proteins for Q84Y91 (Cyanidioschyzon merolae) Explore Q84Y91  Go to UniProtKB:  Q84Y91

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.00 Å
• R-Value Free:  0.411 (Depositor), 0.420 (DCC) 
• R-Value Work:  0.344 (Depositor), 0.350 (DCC) 
• R-Value Observed: 0.351 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.219	α = 90
b = 188.219	β = 90
c = 163.627	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
MOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-08-15 
Deposition Author(s): Bohuszewicz, O., Low, H.H.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	097328/Z/11/Z

Revision History  

• Version 1.0: 2018-08-15
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description