[English] 日本語
Yorodumi
- EMDB-4335: Clathrin Coated Vesicle of 850 angstrom from mouse brain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4335
TitleClathrin Coated Vesicle of 850 angstrom from mouse brain
Map dataClathrin Coated Vesicle from mouse brain
Sample
  • Organelle or cellular component: Clathrin-coated Vesicles
Function / homology
Function and homology information


postsynaptic endocytic zone cytoplasmic component / RHOV GTPase cycle / RHOU GTPase cycle / postsynaptic endocytic zone / Formation of annular gap junctions / Gap junction degradation / presynaptic endocytic zone membrane / Myb complex / clathrin coat of trans-Golgi network vesicle / clathrin vesicle coat ...postsynaptic endocytic zone cytoplasmic component / RHOV GTPase cycle / RHOU GTPase cycle / postsynaptic endocytic zone / Formation of annular gap junctions / Gap junction degradation / presynaptic endocytic zone membrane / Myb complex / clathrin coat of trans-Golgi network vesicle / clathrin vesicle coat / negative regulation of hyaluronan biosynthetic process / LDL clearance / clathrin light chain binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / clathrin complex / Lysosome Vesicle Biogenesis / Retrograde neurotrophin signalling / clathrin coat / VLDLR internalisation and degradation / amyloid-beta clearance by transcytosis / transferrin transport / Recycling pathway of L1 / extrinsic component of synaptic vesicle membrane / clathrin heavy chain binding / clathrin coat of coated pit / mitotic spindle microtubule / Golgi Associated Vesicle Biogenesis / photoreceptor ribbon synapse / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / Clathrin-mediated endocytosis / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / protein serine/threonine kinase binding / retrograde transport, endosome to Golgi / negative regulation of protein localization to plasma membrane / low-density lipoprotein particle receptor binding / clathrin-coated vesicle / ankyrin binding / ubiquitin-specific protease binding / Golgi organization / synaptic vesicle endocytosis / mitotic spindle assembly / regulation of mitotic spindle organization / clathrin-coated pit / T-tubule / heat shock protein binding / receptor-mediated endocytosis / peptide binding / intracellular protein transport / sarcolemma / receptor internalization / synaptic vesicle membrane / mitotic spindle / spindle / autophagy / disordered domain specific binding / melanosome / double-stranded RNA binding / GTPase binding / mitotic cell cycle / myelin sheath / cytoplasmic vesicle / lysosome / endosome / cell cycle / cell division / glutamatergic synapse / protein-containing complex binding / protein kinase binding / structural molecule activity / protein-containing complex / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat ...Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin light chain A / Clathrin heavy chain 1
Similarity search - Component
Biological speciesMus musculoides (Temminck's mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 26.0 Å
AuthorsMilosevic I / Mim C
CitationJournal: Elife / Year: 2018
Title: Clathrin coat controls synaptic vesicle acidification by blocking vacuolar ATPase activity.
Authors: Zohreh Farsi / Sindhuja Gowrisankaran / Matija Krunic / Burkhard Rammner / Andrew Woehler / Eileen M Lafer / Carsten Mim / Reinhard Jahn / Ira Milosevic /
Abstract: Newly-formed synaptic vesicles (SVs) are rapidly acidified by vacuolar adenosine triphosphatases (vATPases), generating a proton electrochemical gradient that drives neurotransmitter loading. ...Newly-formed synaptic vesicles (SVs) are rapidly acidified by vacuolar adenosine triphosphatases (vATPases), generating a proton electrochemical gradient that drives neurotransmitter loading. Clathrin-mediated endocytosis is needed for the formation of new SVs, yet it is unclear when endocytosed vesicles acidify and refill at the synapse. Here, we isolated clathrin-coated vesicles (CCVs) from mouse brain to measure their acidification directly at the single vesicle level. We observed that the ATP-induced acidification of CCVs was strikingly reduced in comparison to SVs. Remarkably, when the coat was removed from CCVs, uncoated vesicles regained ATP-dependent acidification, demonstrating that CCVs contain the functional vATPase, yet its function is inhibited by the clathrin coat. Considering the known structures of the vATPase and clathrin coat, we propose a model in which the formation of the coat surrounds the vATPase and blocks its activity. Such inhibition is likely fundamental for the proper timing of SV refilling.
History
DepositionMar 14, 2018-
Header (metadata) releaseApr 25, 2018-
Map releaseApr 25, 2018-
UpdateApr 25, 2018-
Current statusApr 25, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0187
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0187
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4335.png

Downloads & links

-
Map

FileDownload / File: emd_4335.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClathrin Coated Vesicle from mouse brain
Voxel sizeX=Y=Z: 3.25 Å
Density
Contour LevelBy AUTHOR: 0.0187 / Movie #1: 0.0187
Minimum - Maximum-0.011789018 - 0.07444754
Average (Standard dev.)0.0014637086 (±0.007527677)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 1235.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.253.253.25
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z1235.0001235.0001235.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0120.0740.001

-
Supplemental data

-
Sample components

-
Entire : Clathrin-coated Vesicles

EntireName: Clathrin-coated Vesicles
Components
  • Organelle or cellular component: Clathrin-coated Vesicles

-
Supramolecule #1: Clathrin-coated Vesicles

SupramoleculeName: Clathrin-coated Vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculoides (Temminck's mouse) / Organ: Brain

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.65 mg/mL
BufferpH: 6.5
Component:
ConcentrationNameFormula
100.0 mM2-N-morpholino-ethanesulfonic acid
1.0 mMEGTA
magnesium chlorideMgCl2
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV
DetailsClathrin coated vesicles isolated from mouse brains.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 2836 / Average exposure time: 2.5 sec. / Average electron dose: 23.8 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 43711 / Details: manually picked particles
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 3 / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION / Software - details: 2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D6 (2x6 fold dihedral) / Algorithm: ALGEBRAIC (ARTS) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Software - details: 2 / Number images used: 6114

+
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