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- EMDB-12710: Structural basis for VIPP1 oligomerization and maintenance of thy... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12710 | ||||||||||||||||||||||||
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Title | Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity | ||||||||||||||||||||||||
![]() | C14 refined map | ||||||||||||||||||||||||
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![]() | ESCRT-III / Membrane remodelling / nucleotide hydrolysis / photosynthesis / thylakoid biogenesis / stress response / LIPID BINDING PROTEIN | ||||||||||||||||||||||||
Function / homology | PspA/IM30 / PspA/IM30 family / plasma membrane / Membrane-associated protein Vipp1![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||||||||||||||
![]() | Gupta TK / Klumpe S | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 139.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 42.7 KB | ||
Masks | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 139.5 MB 139.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o3wMC ![]() 7o3xC ![]() 7o3yC ![]() 7o3zC ![]() 7o40C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | C14 refined map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: C14 half map 1
File | emd_12710_half_map_1.map | ||||||||||||
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Annotation | C14 half map 1 | ||||||||||||
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Density Histograms |
-Half map: C14 half map 2
File | emd_12710_half_map_2.map | ||||||||||||
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Annotation | C14 half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : VIPP1 / IM30 complex
Entire | Name: VIPP1 / IM30 complex |
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Components |
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-Supramolecule #1: VIPP1 / IM30 complex
Supramolecule | Name: VIPP1 / IM30 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Protein sll0617
Macromolecule | Name: Protein sll0617 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() Strain: PCC 6803 / Kazusa |
Molecular weight | Theoretical: 28.822145 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: ALFDRLGRVV RANLNDLVSK AEDPEKVLEQ AVIDMQEDLV QLRQAVARTI AEEKRTEQRL NQDTQEAKKW EDRAKLALTN GEENLAREA LARKKSLTDT AAAYQTQLAQ QRTMSENLRR NLAALEAKIS EAKTKKNMLQ ARAKAAKANA ELQQTLGGLG T SSATSAFE ...String: ALFDRLGRVV RANLNDLVSK AEDPEKVLEQ AVIDMQEDLV QLRQAVARTI AEEKRTEQRL NQDTQEAKKW EDRAKLALTN GEENLAREA LARKKSLTDT AAAYQTQLAQ QRTMSENLRR NLAALEAKIS EAKTKKNMLQ ARAKAAKANA ELQQTLGGLG T SSATSAFE RMENKVLDME ATSQAAGELA GFGIENQFAQ LEASSGVEDE LAALKASMAG GALPGTSAAT PQLEAAPVDS SV PANNASQ DDAVIDQELD DLRRRLNNL UniProtKB: Membrane-associated protein Vipp1 |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | Initial model 4whe used for comparative modelling and Rosetta to predict the missing segments |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-7o3w: |