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- EMDB-25007: CryoEM structure of the Caveolin-1 8S complex -

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Basic information

Entry
Database: EMDB / ID: EMD-25007
TitleCryoEM structure of the Caveolin-1 8S complex
Map dataRefined and sharpened volume of the Caveolin-1 8S complex with applied C11 symmetry
Sample
  • Complex: Caveolin-1 8S complex with C11 symmetry.
    • Protein or peptide: Caveolin-1
Keywordscaveolin / caveolae / cryoEM / disc / monotopic proteins / STRUCTURAL PROTEIN
Function / homology
Function and homology information


negative regulation of peptidyl-tyrosine autophosphorylation / caveolar macromolecular signaling complex / protein localization to plasma membrane raft / inward rectifier potassium channel inhibitor activity / negative regulation of inward rectifier potassium channel activity / regulation of peptidase activity / caveola assembly / intracellular nitric oxide homeostasis / protein localization to basolateral plasma membrane / negative regulation of protein tyrosine kinase activity ...negative regulation of peptidyl-tyrosine autophosphorylation / caveolar macromolecular signaling complex / protein localization to plasma membrane raft / inward rectifier potassium channel inhibitor activity / negative regulation of inward rectifier potassium channel activity / regulation of peptidase activity / caveola assembly / intracellular nitric oxide homeostasis / protein localization to basolateral plasma membrane / negative regulation of protein tyrosine kinase activity / negative regulation of cytokine-mediated signaling pathway / insulin receptor internalization / cellular response to hyperoxia / regulation of entry of bacterium into host cell / positive regulation of toll-like receptor 3 signaling pathway / regulation of ruffle assembly / regulation of cardiac muscle cell action potential involved in regulation of contraction / negative regulation of pinocytosis / regulation of membrane repolarization during action potential / regulation of the force of heart contraction by chemical signal / acrosomal membrane / NOSTRIN mediated eNOS trafficking / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of potassium ion transmembrane transport / glandular epithelial cell differentiation / positive regulation of ERAD pathway / FOXO-mediated transcription of cell cycle genes / mammary gland involution / positive regulation of cell adhesion molecule production / vesicle organization / basement membrane organization / patched binding / regulation of fatty acid metabolic process / maintenance of protein location in cell / regulation of smooth muscle contraction / peptidase activator activity / mammary gland development / negative regulation of nitric oxide biosynthetic process / lipid storage / negative regulation of receptor signaling pathway via JAK-STAT / regulation of ventricular cardiac muscle cell action potential / protein tyrosine kinase inhibitor activity / cholesterol transport / caveolin-mediated endocytosis / oxysterol binding / negative regulation of necroptotic process / vasoconstriction / positive regulation of catalytic activity / RHOF GTPase cycle / RHOD GTPase cycle / positive regulation of extrinsic apoptotic signaling pathway / cellular response to misfolded protein / Disassembly of the destruction complex and recruitment of AXIN to the membrane / RND1 GTPase cycle / triglyceride metabolic process / endothelial cell proliferation / cellular response to peptide hormone stimulus / Basigin interactions / RND2 GTPase cycle / RND3 GTPase cycle / cellular response to exogenous dsRNA / cholesterol binding / negative regulation of epithelial cell differentiation / post-transcriptional regulation of gene expression / positive regulation of calcium ion transport into cytosol / RHOB GTPase cycle / muscle cell cellular homeostasis / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-serine phosphorylation / Triglyceride catabolism / RHOC GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / negative regulation of endothelial cell proliferation / regulation of blood coagulation / regulation of heart rate by cardiac conduction / membrane depolarization / CDC42 GTPase cycle / RHOH GTPase cycle / negative regulation of anoikis / positive regulation of gap junction assembly / RHOG GTPase cycle / negative regulation of BMP signaling pathway / positive regulation of cholesterol efflux / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of MAPK cascade / vasculogenesis / canonical Wnt signaling pathway / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / eNOS activation / positive regulation of intrinsic apoptotic signaling pathway / calcium ion homeostasis / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of fibroblast proliferation / cellular response to transforming growth factor beta stimulus / positive regulation of vasoconstriction / skeletal muscle tissue development
Similarity search - Function
Caveolin / Caveolin, conserved site / Caveolin / Caveolins signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPorta JP / Ohi MD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL144131 United States
CitationJournal: Sci Adv / Year: 2022
Title: Molecular architecture of the human caveolin-1 complex.
Authors: Jason C Porta / Bing Han / Alican Gulsevin / Jeong Min Chung / Yelena Peskova / Sarah Connolly / Hassane S Mchaourab / Jens Meiler / Erkan Karakas / Anne K Kenworthy / Melanie D Ohi /
Abstract: Membrane-sculpting proteins shape the morphology of cell membranes and facilitate remodeling in response to physiological and environmental cues. Complexes of the monotopic membrane protein caveolin ...Membrane-sculpting proteins shape the morphology of cell membranes and facilitate remodeling in response to physiological and environmental cues. Complexes of the monotopic membrane protein caveolin function as essential curvature-generating components of caveolae, flask-shaped invaginations that sense and respond to plasma membrane tension. However, the structural basis for caveolin's membrane remodeling activity is currently unknown. Here, we show that, using cryo-electron microscopy, the human caveolin-1 complex is composed of 11 protomers organized into a tightly packed disc with a flat membrane-embedded surface. The structural insights suggest a previously unrecognized mechanism for how membrane-sculpting proteins interact with membranes and reveal how key regions of caveolin-1, including its scaffolding, oligomerization, and intramembrane domains, contribute to its function.
History
DepositionSep 26, 2021-
Header (metadata) releaseMay 25, 2022-
Map releaseMay 25, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25007.png

Downloads & links

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Map

FileDownload / File: emd_25007.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined and sharpened volume of the Caveolin-1 8S complex with applied C11 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 400 pix.
= 392. Å		0.98 Å/pix.
x 400 pix.
= 392. Å		0.98 Å/pix.
x 400 pix.
= 392. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.2541164 - 2.1159697
Average (Standard dev.)0.0001281238 (±0.039439093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 392.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Caveolin-1 8S complex with C11 symmetry.

EntireName: Caveolin-1 8S complex with C11 symmetry.
Components
  • Complex: Caveolin-1 8S complex with C11 symmetry.
    • Protein or peptide: Caveolin-1

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Supramolecule #1: Caveolin-1 8S complex with C11 symmetry.

SupramoleculeName: Caveolin-1 8S complex with C11 symmetry. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Caveolin-1

MacromoleculeName: Caveolin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.494576 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MSGGKYVDSE GHLYTVPIRE QGNIYKPNNK AMADELSEKQ VYDAHTKEID LVNRDPKHLN DDVVKIDFED VIAEPEGTHS FDGIWKASF TTFTVTKYWF YRLLSALFGI PMALIWGIYF AILSFLHIWA VVPCIKSFLI EIQCISRVYS IYVHTVCDPL F EAVGKIFS NVRINLQKEI

UniProtKB: Caveolin-1

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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

Concentration1.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTRIStris(hydroxymethyl)aminomethane
200.0 mMNaClsodium chloride
1.0 mMDTTdithiothreitol
0.05 %DDMn-Dodecyl-beta-Maltoside

Details: Solutions were made fresh for each preparation of 8S particles
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 5 mA glow discharge
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 984 / Average exposure time: 6.0 sec. / Average electron dose: 55.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 40103 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 394900
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C11 (11 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 60615
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 95000 / Software - Name: cryoSPARC (ver. 3.2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 37.8 / Target criteria: Correlation coefficient
Output model

PDB-7sc0:
CryoEM structure of the Caveolin-1 8S complex

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