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- PDB-7o3z: Structural basis for VIPP1 oligomerization and maintenance of thy... -

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Entry
Database: PDB / ID: 7o3z
TitleStructural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity
ComponentsProtein sll0617
KeywordsLIPID BINDING PROTEIN / ESCRT-III / Membrane remodelling / nucleotide hydrolysis / photosynthesis / thylakoid biogenesis / stress response
Function / homologyPspA/IM30 / PspA/IM30 family / plasma membrane / ADENOSINE-5'-DIPHOSPHATE / Membrane-associated protein Vipp1
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsGupta, T.K. / Klumpe, S. / Gries, K. / Strauss, M. / Rudack, T. / Schuller, J.M. / Schroda, M. / Engel, B.D.
Funding support Germany, Japan, 7items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR 2092 EN1194/1-1 Germany
German Research Foundation (DFG)NI 390/9-2 Germany
German Research Foundation (DFG)SCHU 3364 Germany
German Research Foundation (DFG)FOR2092 Schr 617/8-2 Germany
German Research Foundation (DFG)TRR 175/C02 Germany
Ministry of Education, Culture, Sports, Science and Technology (Japan)16H06554 Japan
Japan Society for the Promotion of Science (JSPS)17H03699 Japan
CitationJournal: Cell / Year: 2021
Title: Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity.
Authors: Tilak Kumar Gupta / Sven Klumpe / Karin Gries / Steffen Heinz / Wojciech Wietrzynski / Norikazu Ohnishi / Justus Niemeyer / Benjamin Spaniol / Miroslava Schaffer / Anna Rast / Matthias ...Authors: Tilak Kumar Gupta / Sven Klumpe / Karin Gries / Steffen Heinz / Wojciech Wietrzynski / Norikazu Ohnishi / Justus Niemeyer / Benjamin Spaniol / Miroslava Schaffer / Anna Rast / Matthias Ostermeier / Mike Strauss / Jürgen M Plitzko / Wolfgang Baumeister / Till Rudack / Wataru Sakamoto / Jörg Nickelsen / Jan M Schuller / Michael Schroda / Benjamin D Engel /
Abstract: Vesicle-inducing protein in plastids 1 (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its ...Vesicle-inducing protein in plastids 1 (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its vital membrane-remodeling functions. Here, we use cryo-electron microscopy to determine structures of cyanobacterial VIPP1 rings, revealing how VIPP1 monomers flex and interweave to form basket-like assemblies of different symmetries. Three VIPP1 monomers together coordinate a non-canonical nucleotide binding pocket on one end of the ring. Inside the ring's lumen, amphipathic helices from each monomer align to form large hydrophobic columns, enabling VIPP1 to bind and curve membranes. In vivo mutations in these hydrophobic surfaces cause extreme thylakoid swelling under high light, indicating an essential role of VIPP1 lipid binding in resisting stress-induced damage. Using cryo-correlative light and electron microscopy (cryo-CLEM), we observe oligomeric VIPP1 coats encapsulating membrane tubules within the Chlamydomonas chloroplast. Our work provides a structural foundation for understanding how VIPP1 directs thylakoid biogenesis and maintenance.
History
DepositionApr 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Assembly

Deposited unit
D: Protein sll0617
C: Protein sll0617
E: Protein sll0617
F: Protein sll0617
A: Protein sll0617
B: Protein sll0617
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3607
Polymers172,9336
Non-polymers4271
Water00
1
D: Protein sll0617
C: Protein sll0617
E: Protein sll0617
F: Protein sll0617
A: Protein sll0617
B: Protein sll0617
hetero molecules
x 18


Theoretical massNumber of molelcules
Total (without water)3,120,481126
Polymers3,112,792108
Non-polymers7,69018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation17

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Components

#1: Protein
Protein sll0617 / VIPP1 / IM30 complex


Mass: 28822.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll0617 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q55707
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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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: VIPP1 / IM30 complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: ER2566
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7NAMD2.12model fitting
9PHENIX1.17.1model refinement
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C18 (18 fold cyclic)
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial model 4whe used for comparative modelling and Rosetta to predict the missing segments
Atomic model buildingPDB-ID: 4WHE

4whe


Pdb chain-ID: A / Accession code: 4WHE / Source name: PDB / Type: experimental model

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