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 1.3 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: https://doi.org/10.1038/s41586-018-0211-2
  • Primary Citation of Related Structures:  
    5WP9

  • 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 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

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynamin-1-like protein
A, C, E, G, I
A, C, E, G, I, K, M, O
710Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mitochondrial dynamics protein MID49
B, D, F, H, J
B, D, F, H, J, L, N, P
329Homo sapiensMutation(s): 0 
Gene Names: MIEF2MID49SMCR7
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C03 (Homo sapiens)
Explore Q96C03 
Go to UniProtKB:  Q96C03
PHAROS:  Q96C03
GTEx:  ENSG00000177427 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96C03
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
AA [auth K]
CA [auth M]
EA [auth O]
Q [auth A]
S [auth C]
AA [auth K],
CA [auth M],
EA [auth O],
Q [auth A],
S [auth C],
U [auth E],
W [auth G],
Y [auth I]
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth K]
DA [auth M]
FA [auth O]
R [auth A]
T [auth C]
BA [auth K],
DA [auth M],
FA [auth O],
R [auth A],
T [auth C],
V [auth E],
X [auth G],
Z [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

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 States1DP2GM110772-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM53466
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesS10OD020054 , 1S10OD021741
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM84970

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references