5WP9

Structural Basis of Mitochondrial Receptor Binding and Constriction by Dynamin-Related Protein 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.22 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of mitochondrial receptor binding and constriction by DRP1.

Kalia, R.Wang, R.Y.Yusuf, A.Thomas, P.V.Agard, D.A.Shaw, J.M.Frost, A.

(2018) Nature 558: 401-405

  • DOI: 10.1038/s41586-018-0211-2

  • PubMed Abstract: 
  • Mitochondrial inheritance, genome maintenance and metabolic adaptation depend on organelle fission by dynamin-related protein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogues mitochondrial dynamics proteins of 49 and 51 ...

    Mitochondrial inheritance, genome maintenance and metabolic adaptation depend on organelle fission by dynamin-related protein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogues mitochondrial dynamics proteins of 49 and 51 kDa (MID49 and MID51) and mitochondrial fission factor (MFF); however, the mechanisms by which these proteins recruit and regulate DRP1 are unknown. Here we present a cryo-electron microscopy structure of full-length human DRP1 co-assembled with MID49 and an analysis of structure- and disease-based mutations. We report that GTP induces a marked elongation and rotation of the GTPase domain, bundle-signalling element and connecting hinge loops of DRP1. In this conformation, a network of multivalent interactions promotes the polymerization of a linear DRP1 filament with MID49 or MID51. After co-assembly, GTP hydrolysis and exchange lead to MID receptor dissociation, filament shortening and curling of DRP1 oligomers into constricted and closed rings. Together, these views of full-length, receptor- and nucleotide-bound conformations reveal how DRP1 performs mechanical work through nucleotide-driven allostery.


    Organizational Affiliation

    California Institute for Quantitative Biomedical Research, San Francisco, CA, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.,Department of Biochemistry, University of Utah, Salt Lake City, UT, USA. adam.frost@ucsf.edu.,Howard Hughes Medical Institute, Salt Lake City, UT, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA. adam.frost@ucsf.edu.,Chan Zuckerberg Biohub, San Francisco, CA, USA. adam.frost@ucsf.edu.,Howard Hughes Medical Institute, San Francisco, CA, USA.,California Institute for Quantitative Biomedical Research, San Francisco, CA, USA. adam.frost@ucsf.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dynamin-1-like protein
A, C, E, G, I, K, M, O
710Homo sapiensMutation(s): 0 
Gene Names: DNM1L (DLP1, DRP1)
EC: 3.6.5.5
Find proteins for O00429 (Homo sapiens)
Go to Gene View: DNM1L
Go to UniProtKB:  O00429
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial dynamics protein MID49
B, D, F, H, J, L, N, P
329Homo sapiensMutation(s): 0 
Gene Names: MIEF2 (MID49, SMCR7)
Find proteins for Q96C03 (Homo sapiens)
Go to Gene View: MIEF2
Go to UniProtKB:  Q96C03
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GCP
Query on GCP

Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.22 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1DP2GM110772-01
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM53466
National Institutes of Health/National Human Genome Research InstituteUnited StatesS10OD020054 , 1S10OD021741
National Institutes of Health/National Institute of General Medical SciencesGM84970

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Type: Data collection, Database references