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- EMDB-47023: CryoEM structure of the Salpingoeca rosetta caveolin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47023
TitleCryoEM structure of the Salpingoeca rosetta caveolin complex
Map dataSalpingoeca rosetta caveolin complex
Sample
  • Complex: S. rosetta caveolin complex
    • Protein or peptide: Caveolin
KeywordsMembrane-shaping protein / monotonic membrane protein / MEMBRANE PROTEIN
Function / homologyCaveolin / Caveolin / caveola assembly / caveola / molecular adaptor activity / Golgi membrane / Caveolin
Function and homology information
Biological speciesSalpingoeca rosetta (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsConnolly SM / Ohi MD
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47023.png

Downloads & links

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Map

FileDownload / File: emd_47023.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSalpingoeca rosetta caveolin complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 320 pix.
= 277.44 Å		0.87 Å/pix.
x 320 pix.
= 277.44 Å		0.87 Å/pix.
x 320 pix.
= 277.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.867 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.029
Minimum - Maximum-0.10132323 - 0.20352994
Average (Standard dev.)0.00089664385 (±0.00593988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 277.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Salpingoeca rosetta caveolin complex half map A

Fileemd_47023_half_map_1.map
AnnotationSalpingoeca rosetta caveolin complex half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Salpingoeca rosetta caveolin complex half map B

Fileemd_47023_half_map_2.map
AnnotationSalpingoeca rosetta caveolin complex half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. rosetta caveolin complex

EntireName: S. rosetta caveolin complex
Components
  • Complex: S. rosetta caveolin complex
    • Protein or peptide: Caveolin

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Supramolecule #1: S. rosetta caveolin complex

SupramoleculeName: S. rosetta caveolin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salpingoeca rosetta (eukaryote)

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Macromolecule #1: Caveolin

MacromoleculeName: Caveolin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Salpingoeca rosetta (eukaryote)
Molecular weightTheoretical: 25.605049 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSYHKENTPL TAGSQAASSS TASYQTPPYA PPSSVNHQQQ QQARAAAPSY VGPTPTSTTT YPTIFTPGGF GAPPPSDPEA EEKYIERQL KYLGPISQVS DAYRLDTTTL KIEFDDSFPE VSKPGPALES VRKLNRILYE GMSDAIHIIF SLFLGFLAAI T VGFFMGMA ...String:
MSYHKENTPL TAGSQAASSS TASYQTPPYA PPSSVNHQQQ QQARAAAPSY VGPTPTSTTT YPTIFTPGGF GAPPPSDPEA EEKYIERQL KYLGPISQVS DAYRLDTTTL KIEFDDSFPE VSKPGPALES VRKLNRILYE GMSDAIHIIF SLFLGFLAAI T VGFFMGMA RFMYTYMAGP FNQLMFLLIA SLAPSWRAFF RAGMDPIFES GSLALSNIQV RLGMEGKARH KELKD

UniProtKB: Caveolin

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 59.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C11 (11 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66202
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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