+Open data
-Basic information
Entry | Database: PDB / ID: 7zw6 | ||||||
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Title | Oligomeric structure of SynDLP | ||||||
Components | Slr0869 protein | ||||||
Keywords | LIPID BINDING PROTEIN / BDLP / cyanobacteria / membrane remodeling | ||||||
Function / homology | Mitofusin family / Dynamin, N-terminal / Dynamin family / GTPase activity / GTP binding / P-loop containing nucleoside triphosphate hydrolase / Slr0869 protein Function and homology information | ||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Gewehr, L. / Junglas, B. / Jilly, R. / Franz, J. / Wenyu, E.Z. / Weidner, T. / Bonn, M. / Sachse, C. / Schneider, D. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: SynDLP is a dynamin-like protein of Synechocystis sp. PCC 6803 with eukaryotic features. Authors: Lucas Gewehr / Benedikt Junglas / Ruven Jilly / Johannes Franz / Wenyu Eva Zhu / Tobias Weidner / Mischa Bonn / Carsten Sachse / Dirk Schneider / Abstract: Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin- ...Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin-like protein of the cyanobacterium Synechocystis sp. PCC 6803, forms ordered oligomers in solution. The 3.7 Å resolution cryo-EM structure of SynDLP oligomers reveals the presence of oligomeric stalk interfaces typical for eukaryotic dynamin-like proteins. The bundle signaling element domain shows distinct features, such as an intramolecular disulfide bridge that affects the GTPase activity, or an expanded intermolecular interface with the GTPase domain. In addition to typical GD-GD contacts, such atypical GTPase domain interfaces might be a GTPase activity regulating tool in oligomerized SynDLP. Furthermore, we show that SynDLP interacts with and intercalates into membranes containing negatively charged thylakoid membrane lipids independent of nucleotides. The structural characteristics of SynDLP oligomers suggest it to be the closest known bacterial ancestor of eukaryotic dynamin. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zw6.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7zw6.ent.gz | 1023.3 KB | Display | PDB format |
PDBx/mmJSON format | 7zw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zw6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7zw6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7zw6_validation.xml.gz | 172.2 KB | Display | |
Data in CIF | 7zw6_validation.cif.gz | 255.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/7zw6 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/7zw6 | HTTPS FTP |
-Related structure data
Related structure data | 14993MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 93705.398 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr0869 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami 2 (DE3) / References: UniProt: P73765 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: filamentous homo-oligomer of SynDLP / Type: CELL / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta-gami 2 (DE3) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Blotting force -10 Blotting time 3 s |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 49000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 26.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8322 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 977199 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 119.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS |
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