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

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Basic information

Entry
Database: PDB / ID: 7sc0
TitleCryoEM structure of the Caveolin-1 8S complex
ComponentsCaveolin-1
KeywordsSTRUCTURAL PROTEIN / caveolin / caveolae / cryoEM / disc / monotopic proteins
Function / homology
Function and homology information


caveolar macromolecular signaling complex / protein localization to plasma membrane raft / inward rectifier potassium channel inhibitor activity / nitric-oxide synthase inhibitor activity / protein localization to basolateral plasma membrane / intracellular nitric oxide homeostasis / negative regulation of cytokine-mediated signaling pathway / cellular response to hyperoxia / caveola assembly / insulin receptor internalization ...caveolar macromolecular signaling complex / protein localization to plasma membrane raft / inward rectifier potassium channel inhibitor activity / nitric-oxide synthase inhibitor activity / protein localization to basolateral plasma membrane / intracellular nitric oxide homeostasis / negative regulation of cytokine-mediated signaling pathway / cellular response to hyperoxia / caveola assembly / insulin receptor internalization / regulation of entry of bacterium into host cell / regulation of ruffle assembly / positive regulation of toll-like receptor 3 signaling pathway / regulation of cardiac muscle cell action potential involved in regulation of contraction / negative regulation of pinocytosis / regulation of membrane repolarization during action potential / positive regulation of cell adhesion molecule production / acrosomal membrane / regulation of the force of heart contraction by chemical signal / glandular epithelial cell differentiation / negative regulation of potassium ion transmembrane transport / FOXO-mediated transcription of cell cycle genes / NOSTRIN mediated eNOS trafficking / positive regulation of ERAD pathway / mammary gland involution / basement membrane organization / peptidase activator activity / maintenance of protein location in cell / patched binding / vesicle organization / regulation of fatty acid metabolic process / negative regulation of nitric oxide biosynthetic process / regulation of smooth muscle contraction / negative regulation of receptor signaling pathway via JAK-STAT / regulation of ventricular cardiac muscle cell action potential / mammary gland development / lipid storage / negative regulation of necroptotic process / oxysterol binding / cholesterol transport / caveolin-mediated endocytosis / vasoconstriction / RHOD GTPase cycle / protein tyrosine kinase inhibitor activity / RHOF GTPase cycle / endothelial cell proliferation / positive regulation of extrinsic apoptotic signaling pathway / cellular response to misfolded protein / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cellular response to peptide hormone stimulus / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / Basigin interactions / triglyceride metabolic process / muscle cell cellular homeostasis / cholesterol binding / nitric-oxide synthase binding / RHOB GTPase cycle / post-transcriptional regulation of gene expression / negative regulation of epithelial cell differentiation / positive regulation of calcium ion transport into cytosol / Triglyceride catabolism / cellular response to exogenous dsRNA / regulation of cell communication by electrical coupling involved in cardiac conduction / RHOC GTPase cycle / RHOJ GTPase cycle / regulation of blood coagulation / negative regulation of endothelial cell proliferation / RHOQ GTPase cycle / regulation of heart rate by cardiac conduction / CDC42 GTPase cycle / negative regulation of anoikis / RHOH GTPase cycle / positive regulation of gap junction assembly / negative regulation of BMP signaling pathway / membrane depolarization / RHOG GTPase cycle / positive regulation of cholesterol efflux / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of cytosolic calcium ion concentration / canonical Wnt signaling pathway / negative regulation of MAPK cascade / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / vasculogenesis / calcium ion homeostasis / skeletal muscle tissue development / negative regulation of fibroblast proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of intrinsic apoptotic signaling pathway / cellular response to transforming growth factor beta stimulus / eNOS activation / receptor-mediated endocytosis of virus by host cell / nitric oxide metabolic process / positive regulation of vasoconstriction / lipid droplet / T cell costimulation / lactation
Similarity search - Function
Caveolin / Caveolin, conserved site / Caveolin / Caveolins signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPorta, J.P. / Ohi, M.D. / Kenworthy, A.K. / Karakas, E.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Caveolin-1
B: Caveolin-1
C: Caveolin-1
D: Caveolin-1
E: Caveolin-1
F: Caveolin-1
G: Caveolin-1
H: Caveolin-1
I: Caveolin-1
J: Caveolin-1
K: Caveolin-1


Theoretical massNumber of molelcules
Total (without water)225,44011
Polymers225,44011
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area75600 Å2
ΔGint-680 kcal/mol
Surface area74660 Å2

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Components

#1: Protein
Caveolin-1


Mass: 20494.576 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAV1, CAV / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q03135

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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: Caveolin-1 8S complex with C11 symmetry. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8
Details: Solutions were made fresh for each preparation of 8S particles
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethaneTRIS1
2200 mMsodium chlorideNaCl1
31 mMdithiothreitolDTT1
40.05 %n-Dodecyl-beta-MaltosideDDM1
SpecimenConc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 5 mA glow discharge / Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Calibrated magnification: 40103 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 6 sec. / Electron dose: 55.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 984
Image scansSampling size: 0.98 µm / Width: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2.0particle selection
2Leginon0image acquisitionAutomated image acquisition was setup and carried out in Leginon
4cryoSPARC3.2.0CTF correction
7PHENIX1.19.1_4122model fitting
9cryoSPARC3.2.0initial Euler assignment
10cryoSPARC3.2.0final Euler assignment
11cryoSPARC3.2.0classification
12cryoSPARC3.2.03D reconstruction
13PHENIX1.19.1_4122model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 394900
SymmetryPoint symmetry: C11 (11 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60615 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 37.8 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211990
ELECTRON MICROSCOPYf_angle_d0.43216335
ELECTRON MICROSCOPYf_dihedral_angle_d3.3561507
ELECTRON MICROSCOPYf_chiral_restr0.0431859
ELECTRON MICROSCOPYf_plane_restr0.0031991

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