6JSJ

Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of a trimeric assembly of the mitochondrial dynamin-like GTPase Mgm1.

Yan, L.Qi, Y.Ricketson, D.Li, L.Subramanian, K.Zhao, J.Yu, C.Wu, L.Sarsam, R.Wong, M.Lou, Z.Rao, Z.Nunnari, J.Hu, J.

(2020) Proc Natl Acad Sci U S A 117: 4061-4070

  • DOI: 10.1073/pnas.1919116117
  • Primary Citation of Related Structures:  
    6JSJ

  • PubMed Abstract: 
  • The fusion of inner mitochondrial membranes requires dynamin-like GTPases, Mgm1 in yeast and OPA1 in mammals, but how they mediate membrane fusion is poorly understood. Here, we determined the crystal structure of Saccharomyces cerevisiae short Mgm1 (s-Mgm1) in complex with GDP ...

    The fusion of inner mitochondrial membranes requires dynamin-like GTPases, Mgm1 in yeast and OPA1 in mammals, but how they mediate membrane fusion is poorly understood. Here, we determined the crystal structure of Saccharomyces cerevisiae short Mgm1 (s-Mgm1) in complex with GDP. It revealed an N-terminal GTPase (G) domain followed by two helix bundles (HB1 and HB2) and a unique C-terminal lipid-interacting stalk (LIS). Dimers can form through antiparallel HB interactions. Head-to-tail trimers are built by intermolecular interactions between the G domain and HB2-LIS. Biochemical and in vivo analyses support the idea that the assembly interfaces observed here are native and critical for Mgm1 function. We also found that s-Mgm1 interacts with negatively charged lipids via both the G domain and LIS. Based on these observations, we propose that membrane targeting via the G domain and LIS facilitates the in cis assembly of Mgm1, potentially generating a highly curved membrane tip to allow inner membrane fusion.


    Organizational Affiliation

    College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dynamin-like GTPase MGM1, mitochondrialA, B, C698Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MGM1MDM17YOR211CYOR50-1
UniProt
Find proteins for P32266 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32266 
Go to UniProtKB:  P32266
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A], N [auth B], Y [auth C]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
IOD
Query on IOD

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , E [auth A] , EA [auth C] , F [auth A] , G [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  E [auth A],  EA [auth C],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Z [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.94α = 90
b = 152.94β = 90
c = 236.15γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-04-08 
  • Released Date: 2020-02-19 
  • Deposition Author(s): Yan, L., Li, L.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFC0840302
National Natural Science Foundation of China (NSFC)China31700659

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2020-03-11
    Changes: Database references