8T0R | pdb_00008t0r

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

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2023-06-01 Released: 2024-05-01 
  • Deposition Author(s): Jimah, J.R., Canagarajah, B.J., Hinshaw, J.E.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.97 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 8T0R

This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 397.17 kDa 
  • Atom Count: 22,544 
  • Modeled Residue Count: 2,784 
  • Deposited Residue Count: 3,504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dynamin-1A [auth b],
B [auth c],
C [auth f],
D [auth g]
876Homo 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

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

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: 3.97 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 1.3: 2025-05-28
    Changes: Data collection, Structure summary