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 

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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: https://doi.org/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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dynamin-like GTPase MGM1, mitochondrial
A, B, C
698Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MGM1, MDM17, YOR211C, YOR50-1
UniProt
Find proteins for P32266 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32266 
Go to UniProtKB:  P32266
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32266
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
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]
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

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Entry History & Funding Information

Deposition Data

  • 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