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- EMDB-47022: CryoEM structure of the Strongylocentrotus purpuratus caveolin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47022
TitleCryoEM structure of the Strongylocentrotus purpuratus caveolin complex
Map dataS. purpuratus caveolin complex
Sample
  • Complex: S. purpuratus caveolin complex
    • Protein or peptide: Caveolin
KeywordsMembrane-shaping protein / monotopic membrane protein / MEMBRANE PROTEIN
Function / homologyCaveolin / Caveolin / caveola assembly / caveola / molecular adaptor activity / Golgi membrane / Caveolin
Function and homology information
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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: To Be Published
Title: Evolutionarily diverse caveolins share a common structural framework built around amphipathic discs
Authors: Han B / Connolly SM / Wilson LFL / Schultz D / Gulsevin A / Meiler J / Karakas E / Ohi MD / Kenworthy AK
History
DepositionSep 16, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47022.png

Downloads & links

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Map

FileDownload / File: emd_47022.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS. purpuratus caveolin complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 352 pix.
= 390.368 Å		1.11 Å/pix.
x 352 pix.
= 390.368 Å		1.11 Å/pix.
x 352 pix.
= 390.368 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.109 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-1.3933355 - 2.7009099
Average (Standard dev.)0.0018408423 (±0.0495946)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 390.36798 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: S. purpuratus caveolin half map B

Fileemd_47022_half_map_1.map
AnnotationS. purpuratus caveolin half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: S. purpuratus caveolin half map A

Fileemd_47022_half_map_2.map
AnnotationS. purpuratus caveolin half map A
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. purpuratus caveolin complex

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

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Supramolecule #1: S. purpuratus caveolin complex

SupramoleculeName: S. purpuratus caveolin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)

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Macromolecule #1: Caveolin

MacromoleculeName: Caveolin / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Molecular weightTheoretical: 17.980814 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MELIHPENGP SGTVQVPLIQ GVDQSDTEDV YRLSPHVTTG FADTFKESND IMGFSFMEKV NGAIYKYTHF AFYAVLNLLL APFIAFSFG LSFAVMHFAV VWFVQPIMKL YYVWLRVFNL AYEPALRLVC DPIHRSIALI LSGIKGQFKM NSSDVKTSQV

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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 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: 81000
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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135462
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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