3ZYS

Human dynamin 1 deltaPRD polymer stabilized with GMPPCP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.2 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A Pseudoatomic Model of the Dynamin Polymer Identifies a Hydrolysis-Dependent Powerstroke.

Chappie, J.S.Mears, J.A.Fang, S.Leonard, M.Schmid, S.L.Milligan, R.A.Hinshaw, J.E.Dyda, F.

(2011) Cell 147: 209

  • DOI: https://doi.org/10.1016/j.cell.2011.09.003
  • Primary Citation of Related Structures:  
    3ZYC, 3ZYS

  • PubMed Abstract: 

    The GTPase dynamin catalyzes membrane fission by forming a collar around the necks of clathrin-coated pits, but the specific structural interactions and conformational changes that drive this process remain a mystery. We present the GMPPCP-bound structures of the truncated human dynamin 1 helical polymer at 12.2 Å and a fusion protein, GG, linking human dynamin 1's catalytic G domain to its GTPase effector domain (GED) at 2.2 Å. The structures reveal the position and connectivity of dynamin fragments in the assembled structure, showing that G domain dimers only form between tetramers in sequential rungs of the dynamin helix. Using chemical crosslinking, we demonstrate that dynamin tetramers are made of two dimers, in which the G domain of one molecule interacts in trans with the GED of another. Structural comparison of GG(GMPPCP) to the GG transition-state complex identifies a hydrolysis-dependent powerstroke that may play a role in membrane-remodeling events necessary for fission.


  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DYNAMIN-1
A, D
353Homo sapiensMutation(s): 1 
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
INTERFERON-INDUCED GTP-BINDING PROTEIN MX1
B, E
662Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P20591 (Homo sapiens)
Explore P20591 
Go to UniProtKB:  P20591
PHAROS:  P20591
GTEx:  ENSG00000157601 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20591
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DYNAMIN-1
C, F
113Homo sapiensMutation(s): 0 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.2 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Other
  • Version 1.2: 2013-09-18
    Changes: Derived calculations, Source and taxonomy
  • Version 1.3: 2017-08-23
    Changes: Data collection
  • Version 1.4: 2019-10-23
    Changes: Data collection, Other
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description