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- PDB-7zw6: Oligomeric structure of SynDLP -

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Basic information

Entry
Database: PDB / ID: 7zw6
TitleOligomeric structure of SynDLP
ComponentsSlr0869 protein
KeywordsLIPID BINDING PROTEIN / BDLP / cyanobacteria / membrane remodeling
Function / homologyMitofusin family / Dynamin, N-terminal / Dynamin family / GTPase activity / GTP binding / P-loop containing nucleoside triphosphate hydrolase / Slr0869 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGewehr, L. / Junglas, B. / Jilly, R. / Franz, J. / Wenyu, E.Z. / Weidner, T. / Bonn, M. / Sachse, C. / Schneider, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: 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
DepositionMay 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Slr0869 protein
B: Slr0869 protein
C: Slr0869 protein
D: Slr0869 protein
E: Slr0869 protein
F: Slr0869 protein
G: Slr0869 protein
H: Slr0869 protein


Theoretical massNumber of molelcules
Total (without water)749,6438
Polymers749,6438
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "A"
d_7ens_1chain "G"
d_8ens_1chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METSERF1 - 793
d_21ens_1METSERC1 - 793
d_31ens_1METSERD1 - 793
d_41ens_1METSERE1 - 793
d_51ens_1METSERA1 - 793
d_61ens_1METSERB1 - 793
d_71ens_1METSERG1 - 793
d_81ens_1METSERH1 - 793

NCS oper:
IDCodeMatrixVector
1given(-0.990075053281, 0.00946364169006, -0.140220641691), (0.0122469311332, -0.988125015905, -0.153163199303), (-0.14000500544, -0.153360335253, 0.978202027202)477.930526561, 503.658866497, 72.8313507496
2given(0.989924281408, -0.010008758035, 0.141243555042), (-0.0117252213683, 0.988278793239, 0.152208889416), (-0.141111432074, -0.152331387429, 0.978203819325)-87.176350898, -112.815972339, 72.8433440765
3given(0.997634874228, 0.000460015775395, 0.0687346063503), (-0.00548832218629, 0.997317975254, 0.0729844815983), (-0.0685166844223, -0.0731891017848, 0.994961717523)-45.1865581278, -56.7661723129, 31.1014840495
4given(-0.997144530836, 0.000615924349718, 0.0755142719059), (0.00471981758056, -0.997503447544, 0.0704598854624), (0.0753691445241, 0.0706151030203, 0.994652200158)343.399997438, 331.233618377, -24.1635426573
5given(-0.999999092631, 0.00042418902953, -0.00127859345736), (-0.000424254909186, -0.99999990869, 5.12543154753E-5), (-0.0012785715991, 5.17967185199E-5, 0.999999181286)390.965153545, 390.839455788, 0.262600308243
6given(0.99725740948, -0.000708897222376, -0.0740078151469), (-0.00456527257318, 0.997460773719, -0.0710715356396), (0.0738702749718, 0.0712144813684, 0.994721910947)47.1843861146, 59.6352491211, -23.9426213747
7given(-0.997742510217, -0.00176344933691, -0.0671325074245), (0.00682925030844, -0.997137139809, -0.0753052837082), (-0.0668075193889, -0.0755937474966, 0.99489815594)435.90982603, 447.66020333, 31.2973864252

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Components

#1: Protein
Slr0869 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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: filamentous homo-oligomer of SynDLP / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta-gami 2 (DE3)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMmagnesium chlorideMgCl21
27.5 mMpotassium chlorideKCl1
320 mMHEPESHEPES1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Blotting force -10 Blotting time 3 s

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 49000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM software
IDNameCategory
2EPUimage acquisition
3cryoSPARCimage acquisition
8UCSF ChimeraXmodel fitting
9ISOLDEmodel fitting
11Cootmodel refinement
12ISOLDEmodel refinement
13PHENIXmodel refinement
14cryoSPARCinitial Euler assignment
15cryoSPARCfinal Euler assignment
17cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 977199 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 119.29 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002451736
ELECTRON MICROSCOPYf_angle_d0.515769864
ELECTRON MICROSCOPYf_chiral_restr0.03577792
ELECTRON MICROSCOPYf_plane_restr0.00439248
ELECTRON MICROSCOPYf_dihedral_angle_d3.60827008
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FELECTRON MICROSCOPYNCS constraints2.32310826048E-12
ens_1d_3FELECTRON MICROSCOPYNCS constraints1.73368219149E-12
ens_1d_4FELECTRON MICROSCOPYNCS constraints6.10773541231E-11
ens_1d_5FELECTRON MICROSCOPYNCS constraints6.62620731208E-12
ens_1d_6FELECTRON MICROSCOPYNCS constraints3.01461110004E-11
ens_1d_7FELECTRON MICROSCOPYNCS constraints3.24357349982E-12
ens_1d_8FELECTRON MICROSCOPYNCS constraints1.70887147996E-12

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