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- EMDB-0122: Cryo-EM structure of the hub of the 32 triskelia sweet potato cla... -

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Basic information

Entry
Database: EMDB / ID: EMD-0122
TitleCryo-EM structure of the hub of the 32 triskelia sweet potato clathrin coat complex
Map data
Sample
  • Complex: Assembly of clathrin heavy and light chain into coat complexes
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.79 Å
AuthorsMorris KL / Smith CJ
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly.
Authors: Kyle L Morris / Joseph R Jones / Mary Halebian / Shenping Wu / Michael Baker / Jean-Paul Armache / Amaurys Avila Ibarra / Richard B Sessions / Alexander D Cameron / Yifan Cheng / Corinne J Smith /
Abstract: Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. ...Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. We present the cryo-EM structure and molecular model of assembled porcine clathrin, providing insights into interactions that stabilize key elements of the clathrin lattice, namely, between adjacent heavy chains, at the light chain-heavy chain interface and within the trimerization domain. Furthermore, we report cryo-EM maps for five different clathrin cage architectures. Fitting structural models to three of these maps shows that their assembly requires only a limited range of triskelion leg conformations, yet inherent flexibility is required to maintain contacts. Analysis of the protein-protein interfaces shows remarkable conservation of contact sites despite architectural variation. These data reveal a universal mode of clathrin assembly that allows variable cage architecture and adaptation of coated vesicle size and shape during clathrin-mediated vesicular trafficking or endocytosis.
History
DepositionJul 10, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseOct 2, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.108
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.108
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0122.png

Downloads & links

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Map

FileDownload / File: emd_0122.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 256 pix.
= 436.48 Å		1.71 Å/pix.
x 256 pix.
= 436.48 Å		1.71 Å/pix.
x 256 pix.
= 436.48 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.705 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.108 / Movie #1: 0.108
Minimum - Maximum-0.069263786 - 0.1854125
Average (Standard dev.)0.0017727873 (±0.012002997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 436.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7051.7051.705
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z436.480436.480436.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0690.1850.002

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Supplemental data

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Mask #1

Fileemd_0122_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Post processed map from resolution measurement.

Fileemd_0122_additional.map
AnnotationPost processed map from resolution measurement.
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Additional map: Post processed map from resolution measurement.

Fileemd_0122_additional_1.map
AnnotationPost processed map from resolution measurement.
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Half map: Soft spherical masked (diameter 320A) applied to remove...

Fileemd_0122_half_map_1.map
AnnotationSoft spherical masked (diameter 320A) applied to remove artifactual density prior to resolution measurement.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Soft spherical masked (diameter 320A) applied to remove...

Fileemd_0122_half_map_2.map
AnnotationSoft spherical masked (diameter 320A) applied to remove artifactual density prior to resolution measurement.
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Assembly of clathrin heavy and light chain into coat complexes

EntireName: Assembly of clathrin heavy and light chain into coat complexes
Components
  • Complex: Assembly of clathrin heavy and light chain into coat complexes

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Supramolecule #1: Assembly of clathrin heavy and light chain into coat complexes

SupramoleculeName: Assembly of clathrin heavy and light chain into coat complexes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Sus scrofa (pig) / Organ: BRAIN
Molecular weightTheoretical: 540 KDa

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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

Concentration6.32 mg/mL
BufferpH: 6.4
Component:
ConcentrationFormulaName
100.0 mMC6H13NO4SMES
1.5 mMMgCl2Magnesium chloride
0.2 mMC14H24N2O10EGTA
0.02 w/vNaN3Sodium azide
VitrificationCryogen name: ETHANE-PROPANE / Instrument: HOMEMADE PLUNGER
Details: 3 uL applied to a grid at room temperature and humidity. 3 second hand blot and plunge..
DetailsClathrin coat complexes, end point assembly exhibiting architectural heterogeneity

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 82111 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0032 µm / Nominal defocus min: 0.0014 µm
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: 12785
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER
Details: Initial model and angles come from localised reconstruction of the hub (Ilca 2015)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 56352
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Details: Initial model and angles come from localised reconstruction of the hub (Ilca 2015)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient

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