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- PDB-9em8: Oligomeric structure of SynDLP in presence of GDP -

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Basic information

Entry
Database: PDB / ID: 9em8
TitleOligomeric structure of SynDLP in presence of GDP
ComponentsSlr0869 protein
KeywordsLIPID BINDING PROTEIN / BDLP / cyanobacteria / membrane remodeling / GTPase
Function / homologyMitofusin family / Dynamin, N-terminal / Dynamin family / GTPase activity / GTP binding / P-loop containing nucleoside triphosphate hydrolase / membrane / Slr0869 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJunglas, B. / Gewehr, L. / Schoennenbeck, P. / Schneider, D. / Sachse, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Cell Rep / Year: 2024
Title: Structural basis for GTPase activity and conformational changes of the bacterial dynamin-like protein SynDLP.
Authors: Benedikt Junglas / Lucas Gewehr / Lara Mernberger / Philipp Schönnenbeck / Ruven Jilly / Nadja Hellmann / Dirk Schneider / Carsten Sachse /
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 ...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.
History
DepositionMar 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 2 - 793 / Label seq-ID: 2 - 793

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH

NCS oper:
IDCodeMatrixVector
1given(0.997399978188, -0.0111068239667, 0.0712033845534), (0.00645336821343, 0.997847796001, 0.0652543489272), (-0.071774908911, -0.0646251845381, 0.995325046391)-42.0049751204, -58.660491617, 30.1891898365
2given(0.985294055666, -0.0190984264917, 0.169796566443), (-0.000854348438713, 0.993170634747, 0.116667734893), (-0.17086513383, -0.11509709111, 0.978548805967)-88.061640442, -111.536173531, 71.1709792682
3given(0.995526861191, 0.0117556394436, -0.0937447256555), (-0.0183200507809, 0.997415511621, -0.0694742608197), (0.0926857291407, 0.0708809009419, 0.993169297499)47.6151128893, 62.5760880676, -27.8269228021
4given(-0.987664484721, 0.0127050524687, -0.156068726087), (0.00654077115227, -0.992485466947, -0.122187627079), (-0.1564483427, -0.121701189559, 0.980159546465)478.505307898, 501.834416609, 69.411558568
5given(-0.997380981445, 0.00891709469393, -0.0717750881149), (-0.00415763549506, -0.99779844604, -0.0661889352283), (-0.0722072843886, -0.0657171705248, 0.995222267425)433.832944895, 449.485391324, 30.6343765486
6given(-0.999982771424, -0.00114707589672, 0.00575682829413), (0.00115529812962, -0.999998317136, 0.00142513528429), (0.00575518386784, 0.0014317615842, 0.999982413804)390.328728485, 390.383998443, -1.59312411377
7given(-0.995517213776, -0.00608747111384, 0.0943844254645), (0.0119604913186, -0.998017862676, 0.061784240928), (0.0938212327901, 0.0626361594853, 0.993616771096)342.386862933, 331.238503028, -26.3980914822

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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 in presence of GDP
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
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 44.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 395948 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 92.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001451672
ELECTRON MICROSCOPYf_angle_d0.356169784
ELECTRON MICROSCOPYf_chiral_restr0.03237784
ELECTRON MICROSCOPYf_plane_restr0.00269240
ELECTRON MICROSCOPYf_dihedral_angle_d9.406719616
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints5.4177810125E-11
ens_1d_3AELECTRON MICROSCOPYNCS constraints7.3859536773E-13
ens_1d_4AELECTRON MICROSCOPYNCS constraints1.11461548793E-12
ens_1d_5AELECTRON MICROSCOPYNCS constraints4.73880356652E-13
ens_1d_6AELECTRON MICROSCOPYNCS constraints4.94209476904E-13
ens_1d_7AELECTRON MICROSCOPYNCS constraints3.17941336569E-12
ens_1d_8AELECTRON MICROSCOPYNCS constraints8.73842194197E-13

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