8SZ8

Cryo-EM of the GDP-bound human dynamin polymer assembled on the membrane in the super constricted state (full helix)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission.

Jimah, J.R.Kundu, N.Stanton, A.E.Sochacki, K.A.Canagarajah, B.Chan, L.Strub, M.P.Wang, H.Taraska, J.W.Hinshaw, J.E.

(2024) Dev Cell 59: 1783

  • DOI: https://doi.org/10.1016/j.devcel.2024.04.008
  • Primary Citation of Related Structures:  
    8SXZ, 8SZ4, 8SZ7, 8SZ8, 8T0K, 8T0R, 8TYM, 8TYN

  • PubMed Abstract: 

    Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.


  • Organizational Affiliation

    Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: jimah@princeton.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dynamin-1A [auth b],
B [auth c],
C [auth f],
D [auth g]
754Homo sapiensMutation(s): 1 
Gene Names: DNM1DNM
EC: 3.6.5.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q05193 (Homo sapiens)
Explore Q05193 
Go to UniProtKB:  Q05193
PHAROS:  Q05193
GTEx:  ENSG00000106976 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05193
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth b],
G [auth c],
I [auth f],
K [auth g]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
F [auth b],
H [auth c],
J [auth f],
L [auth g]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 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 Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesZIADK060100
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM140220
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR00GM140220

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references
  • Version 1.2: 2024-08-07
    Changes: Data collection, Database references