9EM8 | pdb_00009em8

Oligomeric structure of SynDLP in presence of GDP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history

Literature

Structural basis for GTPase activity and conformational changes of the bacterial dynamin-like protein SynDLP.

Junglas, B.Gewehr, L.Mernberger, L.Schonnenbeck, P.Jilly, R.Hellmann, N.Schneider, D.Sachse, C.

(2024) Cell Rep 43: 114657-114657

  • DOI: https://doi.org/10.1016/j.celrep.2024.114657
  • Primary Citation Related Structures: 
    9EM7, 9EM8, 9EM9

  • PubMed Abstract: 

    SynDLP, a dynamin-like protein (DLP) encoded in the cyanobacterium Synechocystis sp. PCC 6803, has recently been identified to be structurally highly similar to eukaryotic dynamins. To elucidate structural changes during guanosine triphosphate (GTP) hydrolysis, we solved the cryoelectron microscopy (cryo-EM) structures of oligomeric full-length SynDLP after addition of guanosine diphosphate (GDP) at 4.1 Å and GTP at 3.6-Å resolution as well as a GMPPNP-bound dimer structure of a minimal G-domain construct of SynDLP at 3.8-Å resolution. In comparison with what has been seen in the previously resolved apo structure, we found that the G-domain is tilted upward relative to the stalk upon GTP hydrolysis and that the G-domain dimerizes via an additional extended dimerization domain not present in canonical G-domains. When incubated with lipid vesicles, we observed formation of irregular tubular SynDLP assemblies that interact with negatively charged lipids. Here, we provide the structural framework of a series of different functional SynDLP assembly states during GTP turnover.


  • Organizational Affiliation
    • Ernst Ruska-Center for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany.

Macromolecule Content 

  • Total Structure Weight: 749.64 kDa 
  • Atom Count: 50,872 
  • Modeled Residue Count: 6,336 
  • Deposited Residue Count: 6,560 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Slr0869 protein
A, B, C, D, E
A, B, C, D, E, F, G, H
820Synechocystis sp. PCC 6803Mutation(s): 0 
Gene Names: slr0869
UniProt
Find proteins for P73765 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore P73765 
Go to UniProtKB:  P73765
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73765
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release