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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
Function / homology
Function and homology information


negative regulation of peptidyl-tyrosine autophosphorylation / receptor internalization involved in canonical Wnt signaling pathway / 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 / angiotensin-activated signaling pathway involved in heart process / caveola assembly / intracellular nitric oxide homeostasis ...negative regulation of peptidyl-tyrosine autophosphorylation / receptor internalization involved in canonical Wnt signaling pathway / 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 / angiotensin-activated signaling pathway involved in heart process / caveola assembly / intracellular nitric oxide homeostasis / protein localization to basolateral plasma membrane / : / negative regulation of cytokine-mediated signaling pathway / negative regulation of protein tyrosine kinase activity / insulin receptor internalization / regulation of entry of bacterium into host cell / positive regulation of toll-like receptor 3 signaling pathway / cellular response to hyperoxia / negative regulation of nitric-oxide synthase activity / 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 / negative regulation of potassium ion transmembrane transport / acrosomal membrane / regulation of the force of heart contraction by chemical signal / NOSTRIN mediated eNOS trafficking / FOXO-mediated transcription of cell cycle genes / positive regulation of cell adhesion molecule production / mammary gland involution / vesicle organization / basement membrane organization / regulation of fatty acid metabolic process / regulation of smooth muscle contraction / patched binding / maintenance of protein location in cell / negative regulation of tyrosine phosphorylation of STAT protein / peptidase activator activity / 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 / mammary gland development / cholesterol transport / caveolin-mediated endocytosis / negative regulation of necroptotic process / vasoconstriction / RHOF GTPase cycle / RHOD GTPase cycle / triglyceride metabolic process / positive regulation of extrinsic apoptotic signaling pathway / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Basigin interactions / RND1 GTPase cycle / RND2 GTPase cycle / cellular response to peptide hormone stimulus / RND3 GTPase cycle / cholesterol binding / negative regulation of epithelial cell differentiation / positive regulation of calcium ion transport into cytosol / post-transcriptional regulation of gene expression / RHOB GTPase cycle / cellular response to exogenous dsRNA / negative regulation of endothelial cell proliferation / negative regulation of MAPK cascade / positive regulation of catalytic activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / regulation of heart rate by cardiac conduction / Triglyceride catabolism / regulation of blood coagulation / plasma membrane => GO:0005886 / membrane depolarization / positive regulation of gap junction assembly / RHOH GTPase cycle / CDC42 GTPase cycle / positive regulation of cholesterol efflux / negative regulation of BMP signaling pathway / RHOG GTPase cycle / negative regulation of anoikis / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / calcium ion homeostasis / vasculogenesis / negative regulation of peptidyl-serine phosphorylation / eNOS activation / skeletal muscle tissue development / positive regulation of intrinsic apoptotic signaling pathway / positive regulation of vasoconstriction / negative regulation of protein ubiquitination / cellular response to transforming growth factor beta stimulus / RAC1 GTPase cycle / T cell costimulation / regulation of cytosolic calcium ion concentration / cellular response to starvation / lactation
Similarity search - Function
Caveolin / Caveolin-1 / 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 / Kenworthy AK / Karakas E
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-
UpdateMay 25, 2022-
Current statusMay 25, 2022Processing 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
Voxel sizeX=Y=Z: 0.98 Å
Density
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)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)

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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

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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 chloridesodium 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: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / 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
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 FIELDBright-field microscopy / 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
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 - Sampling interval: 0.98 µm / 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

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Image processing

Particle selectionNumber selected: 394900
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0)
Initial 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)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2.0)
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
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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