[English] 日本語
Yorodumi
- EMDB-25007: CryoEM structure of the Caveolin-1 8S complex -

+
Open data


ID or keywords:

Loading...

-
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


caveolar macromolecular signaling complex / protein localization to plasma membrane raft / inward rectifier potassium channel inhibitor activity / negative regulation of inward rectifier potassium channel 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 / negative regulation of inward rectifier potassium channel 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 / 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 / positive regulation of cell adhesion molecule production / regulation of the force of heart contraction by chemical signal / acrosomal membrane / NOSTRIN mediated eNOS trafficking / negative regulation of potassium ion transmembrane transport / glandular epithelial cell differentiation / FOXO-mediated transcription of cell cycle genes / positive regulation of ERAD pathway / mammary gland involution / basement membrane organization / maintenance of protein location in cell / regulation of smooth muscle contraction / peptidase activator activity / patched binding / vesicle organization / regulation of fatty acid metabolic process / negative regulation of nitric oxide biosynthetic process / negative regulation of receptor signaling pathway via JAK-STAT / regulation of ventricular cardiac muscle cell action potential / lipid storage / mammary gland development / negative regulation of necroptotic process / oxysterol binding / cholesterol transport / caveolin-mediated endocytosis / vasoconstriction / protein tyrosine kinase inhibitor activity / RHOD GTPase cycle / 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 / negative regulation of peptidyl-serine phosphorylation / triglyceride metabolic process / muscle cell cellular homeostasis / nitric-oxide synthase binding / cholesterol binding / post-transcriptional regulation of gene expression / RHOB GTPase cycle / negative regulation of epithelial cell differentiation / positive regulation of calcium ion transport into cytosol / cellular response to exogenous dsRNA / Triglyceride catabolism / regulation of cell communication by electrical coupling involved in cardiac conduction / RHOC GTPase cycle / RHOJ GTPase cycle / regulation of blood coagulation / RHOQ GTPase cycle / negative regulation of endothelial cell proliferation / regulation of heart rate by cardiac conduction / negative regulation of anoikis / CDC42 GTPase cycle / RHOH GTPase cycle / positive regulation of gap junction assembly / membrane depolarization / negative regulation of BMP signaling pathway / 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 / vasculogenesis / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / calcium ion homeostasis / positive regulation of intrinsic apoptotic signaling pathway / skeletal muscle tissue development / negative regulation of fibroblast proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / eNOS activation / cellular response to transforming growth factor beta stimulus / receptor-mediated endocytosis of virus by host cell / positive regulation of vasoconstriction / T cell costimulation / lactation / lipid droplet
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

-
Structure visualization

Supplemental images

emd_25007.png

Downloads & links

-
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 °

-
Supplemental data

-
Sample components

-
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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more