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- EMDB-19813: Oligomeric structure of SynDLP in presence of GDP -

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Basic information

Entry
Database: EMDB / ID: EMD-19813
TitleOligomeric structure of SynDLP in presence of GDP
Map data
Sample
  • Cell: filamentous homo-oligomer of SynDLP in presence of GDP
    • Protein or peptide: Slr0869 protein
KeywordsBDLP / cyanobacteria / membrane remodeling / GTPase / LIPID BINDING PROTEIN
Function / homologyMitofusin family / Dynamin, N-terminal / Dynamin family / GTPase activity / P-loop containing nucleoside triphosphate hydrolase / Slr0869 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJunglas B / Gewehr L / Schoennenbeck P / Schneider D / Sachse C
Funding supportEuropean Union, 1 items
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, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19813.png

Downloads & links

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Map

FileDownload / File: emd_19813.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 450 pix.
= 391.05 Å		0.87 Å/pix.
x 450 pix.
= 391.05 Å		0.87 Å/pix.
x 450 pix.
= 391.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.869 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.159
Minimum - Maximum-0.30216601 - 0.6099319
Average (Standard dev.)0.0025123882 (±0.019861968)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 391.05002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : filamentous homo-oligomer of SynDLP in presence of GDP

EntireName: filamentous homo-oligomer of SynDLP in presence of GDP
Components
  • Cell: filamentous homo-oligomer of SynDLP in presence of GDP
    • Protein or peptide: Slr0869 protein

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Supramolecule #1: filamentous homo-oligomer of SynDLP in presence of GDP

SupramoleculeName: filamentous homo-oligomer of SynDLP in presence of GDP
type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: Slr0869 protein

MacromoleculeName: Slr0869 protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 93.705398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKIAPQCQN LREQVNQLIE LLRQEPTLRS QQDTSIVETA LGKALSPRFE IVFAGAFSAG KSMLINALLE RELLYSAEGH ATGTECHIE YANANEERVV LTFLSEAEIR QQALILAKYL NVNVGDLNIN QPEAVKVVSQ YCQKIIAEEG GENKSERAKQ A NALHLLLI ...String:
MSKIAPQCQN LREQVNQLIE LLRQEPTLRS QQDTSIVETA LGKALSPRFE IVFAGAFSAG KSMLINALLE RELLYSAEGH ATGTECHIE YANANEERVV LTFLSEAEIR QQALILAKYL NVNVGDLNIN QPEAVKVVSQ YCQKIIAEEG GENKSERAKQ A NALHLLLI GFEQNRERIN TVQNSTYSMD QLNFSSLAEA AGYARRGANS AVLKRLDYFC NHSLLKDGNV LVDLPGIDAP VK EDAERAY RKIESPDTSA VICVLKPAAA GDMSAEETQL LERISKNHGI RDRVFYVFNR IDDTWYNTQL RQRLEGLIQS QFR DNSRVY KTSGLLGFYG SQVKQTNSST RFGLDSIFAT TIKGFDGEEE TPQFVSEFNN YCANSGKLLS TAFRVSVNGY ETSN ENYVR ILSEWGIPLV DQLIHDSGIE SFRSGIGLYL AEEKYPELFA TLANDLQPLC IALRQFYLEN YRQLDSQPRE IAAMK AQEL TLLNQEMQNL GIEFKKYMSA QINDVVIGND REFDQDFTKL KARMVARLDE LLKTFSVMNA YKRATESHPR NSTAPF IAV LVEALYYLAN ELEDAFIEAI HELVKNFFQR LGDRLRKVDC YHQVYRLVGN DGGIEQLLRR AEEDITKALV NEARTEC DR YVRESPRFYD EGTFSIYQFR QTLQQTSQGY DAQAIVEAEP AIKELLKLDF EPKVFNTVRK NFRQTVNNTL KTHLLPMA E EQAQIILEQY DVARKYREQT LEQDAEEKIA RNSRLQSEIK QKIDLYQTSI VSINECLKAM QIFEQLPVIT ESDITKQAE IVADADFVEI VELEHHHHHH

UniProtKB: Slr0869 protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zw6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 395948
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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