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- EMDB-19814: Structure of SynDLP MGD with GMPPNP -

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Basic information

Entry
Database: EMDB / ID: EMD-19814
TitleStructure of SynDLP MGD with GMPPNP
Map data
Sample
  • Complex: SynDLP MGD
    • Protein or peptide: Slr0869 protein
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsBDLP / cyanobacteria / membrane remodeling / GTPase / LIPID BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_19814.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.)
0.82 Å/pix.
x 450 pix.
= 367.2 Å		0.82 Å/pix.
x 450 pix.
= 367.2 Å		0.82 Å/pix.
x 450 pix.
= 367.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.816 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.926
Minimum - Maximum-7.276525 - 5.9428463
Average (Standard dev.)0.0029141337 (±0.06607237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 367.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SynDLP MGD

EntireName: SynDLP MGD
Components
  • Complex: SynDLP MGD
    • Protein or peptide: Slr0869 protein
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: SynDLP MGD

SupramoleculeName: SynDLP MGD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 59.29141 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 YRQLDSQPGS GSGSG GSKI ARNSRLQSEI KQKIDLYQTS IVSINECLKA MQIFEQLPHH HHHH

UniProtKB: Slr0869 protein, Slr0869 protein

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: OTHER / Details: AlphaFold2 prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219630
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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