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- EMDB-12981: Cryo-EM structure of the 28 triskelia mini clathrin coat complex,... -

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Basic information

Entry
Database: EMDB / ID: EMD-12981
TitleCryo-EM structure of the 28 triskelia mini clathrin coat complex, class 18.
Map data
Sample
  • Complex: Cryo-EM structure of 28 triskelia mini clathrin coat complex, class 18
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / Nef Mediated CD8 Down-regulation / clathrin adaptor complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / Nef Mediated CD8 Down-regulation / clathrin adaptor complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / LDL clearance / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / clathrin-dependent endocytosis / coronary vasculature development / endolysosome membrane / signal sequence binding / Nef Mediated CD4 Down-regulation / aorta development / ventricular septum development / clathrin binding / Recycling pathway of L1 / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / kidney development / intracellular protein transport / clathrin-coated endocytic vesicle membrane / cytoplasmic side of plasma membrane / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / presynapse / postsynapse / Potential therapeutics for SARS / glutamatergic synapse / structural molecule activity / membrane / plasma membrane / cytosol
Similarity search - Function
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 / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat ...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 / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin heavy chain / AP-2 complex subunit beta
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsSmith SM / Smith CJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N008391/1 United Kingdom
CitationJournal: EMBO J / Year: 2021
Title: Multi-modal adaptor-clathrin contacts drive coated vesicle assembly.
Authors: Sarah M Smith / Gabrielle Larocque / Katherine M Wood / Kyle L Morris / Alan M Roseman / Richard B Sessions / Stephen J Royle / Corinne J Smith /
Abstract: Clathrin-coated pits are formed by the recognition of membrane and cargo by the AP2 complex and the subsequent recruitment of clathrin triskelia. A role for AP2 in coated-pit assembly beyond initial ...Clathrin-coated pits are formed by the recognition of membrane and cargo by the AP2 complex and the subsequent recruitment of clathrin triskelia. A role for AP2 in coated-pit assembly beyond initial clathrin recruitment has not been explored. Clathrin binds the β2 subunit of AP2, and several binding sites have been identified, but our structural knowledge of these interactions is incomplete and their functional importance during endocytosis is unclear. Here, we analysed the cryo-EM structure of clathrin cages assembled in the presence of β2 hinge-appendage (β2HA). We find that the β2-appendage binds in at least two positions in the cage, demonstrating that multi-modal binding is a fundamental property of clathrin-AP2 interactions. In one position, β2-appendage cross-links two adjacent terminal domains from different triskelia. Functional analysis of β2HA-clathrin interactions reveals that endocytosis requires two clathrin interaction sites: a clathrin-box motif on the hinge and the "sandwich site" on the appendage. We propose that β2-appendage binding to more than one triskelion is a key feature of the system and likely explains why assembly is driven by AP2.
History
DepositionMay 20, 2021-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0125
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12981.png

Downloads & links

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Map

FileDownload / File: emd_12981.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.78 Å/pix.
x 500 pix.
= 1390. Å		2.78 Å/pix.
x 500 pix.
= 1390. Å		2.78 Å/pix.
x 500 pix.
= 1390. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0125 / Movie #1: 0.0125
Minimum - Maximum-0.0357234 - 0.078229584
Average (Standard dev.)0.00028024055 (±0.0041563096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 1390.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.782.782.78
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z1390.0001390.0001390.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ243257325
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0360.0780.000

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Supplemental data

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Mask #1

Fileemd_12981_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unsharpened map

Fileemd_12981_additional_1.map
AnnotationUnsharpened map
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Half map: #1

Fileemd_12981_half_map_1.map
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Half map: #2

Fileemd_12981_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of 28 triskelia mini clathrin coat complex, class 18

EntireName: Cryo-EM structure of 28 triskelia mini clathrin coat complex, class 18
Components
  • Complex: Cryo-EM structure of 28 triskelia mini clathrin coat complex, class 18

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Supramolecule #1: Cryo-EM structure of 28 triskelia mini clathrin coat complex, class 18

SupramoleculeName: Cryo-EM structure of 28 triskelia mini clathrin coat complex, class 18
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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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

BufferpH: 6.4
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: LEICA EM GP
Details: 3 uL of sample applied to a grid and blotted for 4.5 s before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.0.5)
Final reconstructionApplied symmetry - Point group: T (tetrahedral) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 715
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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