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- PDB-9dn0: CryoEM structure of the Strongylocentrotus purpuratus caveolin complex -

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Basic information

Entry
Database: PDB / ID: 9dn0
TitleCryoEM structure of the Strongylocentrotus purpuratus caveolin complex
ComponentsCaveolin
KeywordsMEMBRANE PROTEIN / Membrane-shaping protein / monotopic membrane protein
Function / homologyCaveolin / Caveolin / caveola assembly / caveola / molecular adaptor activity / Golgi membrane / Caveolin
Function and homology information
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsConnolly, S.M. / Ohi, M.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM151635 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL144131 United States
CitationJournal: J Cell Biol / Year: 2025
Title: Evolutionarily diverse caveolins share a common structural framework built around amphipathic disks.
Authors: Bing Han / Sarah M Connolly / Darrin T Schultz / Louis F L Wilson / Alican Gulsevin / Jens Meiler / Erkan Karakas / Melanie D Ohi / Anne K Kenworthy /
Abstract: Caveolins are a unique family of membrane remodeling proteins present broadly across animals (Metazoa), and in vertebrates form flask-shaped invaginations known as caveolae. While human caveolin-1 ...Caveolins are a unique family of membrane remodeling proteins present broadly across animals (Metazoa), and in vertebrates form flask-shaped invaginations known as caveolae. While human caveolin-1 assembles into an amphipathic disk composed of 11 spirally packed protomers, the structural basis underlying caveolin function across animals remains elusive. Here, we predicted structures for 73 caveolins spanning animal diversity, as well as a newly identified choanoflagellate caveolin from Salpingoeca rosetta. This analysis revealed seven conserved structural elements and a propensity to assemble into amphipathic disks. Cryo-EM structures of caveolins from S. rosetta choanoflagellate and the purple sea urchin Strongylocentrotus purpuratus exhibit striking structural similarities to human caveolin-1, validating the structural predictions. Lastly, tracing the chromosomal evolutionary history of caveolins revealed its parahoxozoan ancestral chromosome and evolutionary branches on which caveolins translocated and expanded. These results show that caveolins possess an ancient structural framework predating Metazoa and provide a new structural paradigm to explore the molecular basis of caveolin function across diverse evolutionary lineages.
History
DepositionSep 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caveolin
B: Caveolin
C: Caveolin
D: Caveolin
E: Caveolin
F: Caveolin
G: Caveolin
H: Caveolin
I: Caveolin
J: Caveolin
K: Caveolin


Theoretical massNumber of molelcules
Total (without water)197,78911
Polymers197,78911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Caveolin


Mass: 17980.814 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Strongylocentrotus purpuratus (purple sea urchin)
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A7M7T4C2
Has protein modificationN

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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: S. purpuratus caveolin complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEM4.0.3image acquisition
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135462 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211451
ELECTRON MICROSCOPYf_angle_d0.54515532
ELECTRON MICROSCOPYf_dihedral_angle_d4.9281474
ELECTRON MICROSCOPYf_chiral_restr0.0421694
ELECTRON MICROSCOPYf_plane_restr0.0041903

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