5YEW

Structural basis for GTP hydrolysis and conformational change of mitofusin 1 in mediating mitochondrial fusion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for GTP hydrolysis and conformational change of MFN1 in mediating membrane fusion

Yan, L.Qi, Y.Huang, X.Yu, C.Lan, L.Guo, X.Rao, Z.Hu, J.Lou, Z.

(2018) Nat Struct Mol Biol 25: 233-243

  • DOI: 10.1038/s41594-018-0034-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Fusion of the outer mitochondrial membrane is mediated by the dynamin-like GTPase mitofusin (MFN). Here, we determined the structure of the minimal GTPase domain (MGD) of human MFN1 in complex with GDP-BeF 3 - . The MGD folds i ...

    Fusion of the outer mitochondrial membrane is mediated by the dynamin-like GTPase mitofusin (MFN). Here, we determined the structure of the minimal GTPase domain (MGD) of human MFN1 in complex with GDP-BeF 3 - . The MGD folds into a canonical GTPase fold with an associating four-helix bundle, HB1, and forms a dimer. A potassium ion in the catalytic core engages GDP and BeF 3 - (GDP-BeF 3 - ). Enzymatic analysis has confirmed that efficient GTP hydrolysis by MFN1 requires potassium. Compared to previously reported MGD structures, the HB1 structure undergoes a major conformational change relative to the GTPase domains, as they move from pointing in opposite directions to point in the same direction, suggesting that a swing of the four-helix bundle can pull tethered membranes closer to achieve fusion. The proposed model is supported by results from in vitro biochemical assays and mitochondria morphology rescue assays in MFN1-deleted cells. These findings offer an explanation for how Charcot-Marie-Tooth neuropathy type 2 A (CMT2A)-causing mutations compromise MFN-mediated fusion.


    Organizational Affiliation

    Collaborative Innovation Center for Biotherapy, Tsinghua University, Tsinghua, China. louzy@mail.tsinghua.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mitofusin-1,Mitofusin-1 fusion protein
A
421Homo sapiensMutation(s): 2 
Gene Names: MFN1
EC: 3.6.5
Find proteins for Q8IWA4 (Homo sapiens)
Go to UniProtKB:  Q8IWA4
NIH Common Fund Data Resources
PHAROS  Q8IWA4
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitofusin-1,Mitofusin-1 fusion protein
B, C
421Homo sapiensMutation(s): 0 
Gene Names: MFN1
EC: 3.6.5
Find proteins for Q8IWA4 (Homo sapiens)
Go to UniProtKB:  Q8IWA4
NIH Common Fund Data Resources
PHAROS  Q8IWA4
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download CCD File 
A, B, C
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
BEF
Query on BEF

Download CCD File 
A, B, C
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
K
Query on K

Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.942α = 90
b = 207.942β = 90
c = 107.893γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
AutoPROCmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Natural Science Foundation of ChinaChina31700659
the National Natural Science Foundation of ChinaChina31225006
the National Natural Science Foundation of ChinaChina81322023

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2018-03-14
    Changes: Database references
  • Version 1.3: 2018-03-21
    Changes: Database references