6JSJ | pdb_00006jsj

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 (Depositor), 0.317 (DCC) 
  • R-Value Work: 
    0.243 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1073/pnas.1919116117
  • Primary Citation 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. 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
    • National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 241.7 kDa 
  • Atom Count: 15,082 
  • Modeled Residue Count: 1,868 
  • Deposited Residue Count: 2,094 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dynamin-like GTPase MGM1, mitochondrial
A, B, C
698Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MGM1
EC: 3.6.5.5
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / 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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.306 (Depositor), 0.317 (DCC) 
  • R-Value Work:  0.243 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
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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Ligand Structure Quality Assessment 


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
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Structure summary