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- EMDB-21616: Hexagonal face of the mini-coat cage for a clathrin coated vesicle -

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Basic information

Entry
Database: EMDB / ID: EMD-21616
TitleHexagonal face of the mini-coat cage for a clathrin coated vesicle
Map dataLow pass filtered
Sample
  • Complex: Natively assembled clathrin coated vesicles
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 Å
AuthorsParaan M / Mendez J / Sharum S / Kurtin D / He H / Stagg S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM108753 United States
CitationJournal: Sci Adv / Year: 2020
Title: The structures of natively assembled clathrin-coated vesicles.
Authors: Paraan M / Mendez J / Sharum S / Kurtin D / He H / Stagg SM
History
DepositionMar 30, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseAug 19, 2020-
UpdateAug 19, 2020-
Current statusAug 19, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.236
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.236
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_21616.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow pass filtered
Voxel sizeX=Y=Z: 2.646 Å
Density
Contour LevelBy AUTHOR: 0.236 / Movie #1: 0.236
Minimum - Maximum-0.17284796 - 1.140737
Average (Standard dev.)0.02552357 (±0.12531416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 793.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.6462.6462.646
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z793.800793.800793.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-205-205-205
NX/NY/NZ411411411
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-0.1731.1410.026

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Supplemental data

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Sample components

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Entire : Natively assembled clathrin coated vesicles

EntireName: Natively assembled clathrin coated vesicles
Components
  • Complex: Natively assembled clathrin coated vesicles

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Supramolecule #1: Natively assembled clathrin coated vesicles

SupramoleculeName: Natively assembled clathrin coated vesicles / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: brain

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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

Concentration6 mg/mL
BufferpH: 6.7
Component:
ConcentrationNameFormula
100.0 mMMES
1.0 mMMagnesium ChlorideMgCl2
1.0 mMEGTA
GridModel: C-flat-2/2 4C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 40.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 800 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 35000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 60000
Details: These are subparticle images that were extracted from particle images. Each minicoat particle has 4 hexagonal faces. From a total of 15000 minicoat particles, 60000 hexagonal faces were ...Details: These are subparticle images that were extracted from particle images. Each minicoat particle has 4 hexagonal faces. From a total of 15000 minicoat particles, 60000 hexagonal faces were extracted. The position of subparticles was calculated by the localized reconstruction script in scipion, and the subparticle images were extracted with RELION extraction tools.
CTF correctionSoftware: (Name: cisTEM (ver. 1), CTFFIND (ver. 4), RELION (ver. 3))
Startup modelType of model: OTHER
Details: A hexagonal face was cut out of the minicoat cage map from the same dataset.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 54880
Initial angle assignmentType: OTHER
Details: Using the Euler angles of the mini-coat cage particles and the position of the hexagonal faces in the map, initial hexagonal face Eulers were calculated.
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2)
Details: Using 2D classification and homogenous refinement tools of cryoSPARC, shifts and Euler angles were refined for binned-by-2 subparticle images.

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