8V8T | pdb_00008v8t

Asymmetrical subunit from a Drp1 lattice on PA nanotubes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.7 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Structure of the Drp1 Lattice on Membrane.

Peng, R.Rochon, K.Hutson, A.N.Stagg, S.M.Mears, J.A.

(2025) J Mol Biology 437: 169125-169125

  • DOI: https://doi.org/10.1016/j.jmb.2025.169125
  • Primary Citation of Related Structures:  
    8V8T

  • PubMed Abstract: 

    Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanisms. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. We identified two states of the Drp1 lattice among the heterogenous dataset representing conformational changes around hinge 1. Additionally, we observed contact between Drp1 and membrane that can be assigned to the variable domain sequence. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.


  • Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynamin-1-like protein
A, B, C, D
743Homo sapiensMutation(s): 0 
Gene Names: DNM1LDLP1DRP1
EC: 3.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for O00429 (Homo sapiens)
Explore O00429 
Go to UniProtKB:  O00429
PHAROS:  O00429
GTEx:  ENSG00000087470 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00429
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 14.7 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM125844
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM108753
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM143805
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF31 GM139324

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references