9KFD | pdb_00009kfd

Truncated Fzo1,GTP-bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 
    0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A special latch in yeast mitofusin guarantees mitochondrial fusion by stabilizing self-assembly.

Huang, S.J.Ma, D.F.Yu, C.Li, J.Tu, X.Huang, Z.Qi, Y.Ou, J.Y.Feng, J.X.Yu, B.Cao, Y.L.Yue, J.X.Hu, J.Li, M.Lu, Y.Yan, L.Gao, S.

(2025) Nat Commun 16: 9644-9644

  • DOI: https://doi.org/10.1038/s41467-025-64646-x
  • Primary Citation of Related Structures:  
    9KFD, 9KFE, 9KFF

  • PubMed Abstract: 

    The mitochondrion is a highly dynamic organelle, constantly undergoing fusion and fission, which are critical processes for the health of cells. Fusion of the outer mitochondrial membrane (OMM) is mediated by the mitofusins belonging to the dynamin superfamily of GTPases. Most eukaryotic organisms possess two cooperatively functioning mitofusins, but yeast has only one mitofusin (Fzo1). How Fzo1 solely catalyzes OMM fusion is unclear. Here, we present crystal structures of truncated Fzo1 (Fzo1 IM ) in different nucleotide-loading states and report a special mechanistic feature of Fzo1 through systematic functional studies. Differing from mammalian mitofusins, Fzo1 contains an extra latch bulge (LB) that is essential for the viability of yeast. Upon GTP loading, Fzo1 IM dimerizes via the GTPase domain and prefers the closed conformation. This state is then locked by the subsequent trans interaction mediated by the LB of each protomer, so that Fzo1 IM remains dimerized in the closed conformation even after GTP hydrolysis. This special mechanistic feature may be relevant to the previous observation that degradation of Fzo1 by the ubiquitin-proteasome system is required for mitochondrial fusion. Our study reveals how mitochondrial fusion in yeast is efficiently ensured with limited GTP consumption, which broadens current understanding of this fundamental biological process.


  • Organizational Affiliation
    • State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mitofusin FZO1
A, B
468Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: FZO1YBR179CYBR1241
EC: 3.6.5
UniProt
Find proteins for P38297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38297 
Go to UniProtKB:  P38297
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38297
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free:  0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.404α = 90
b = 174.404β = 90
c = 127.001γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371258
National Natural Science Foundation of China (NSFC)China82341073
National Natural Science Foundation of China (NSFC)China2320103002
National Natural Science Foundation of China (NSFC)China82173098

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Database references