Biotechnology and Biological Sciences Research Council (BBSRC)
BB/N008391/1
United Kingdom
Citation
Journal: 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
Deposition
May 21, 2021
-
Header (metadata) release
Aug 11, 2021
-
Map release
Aug 11, 2021
-
Update
Jul 10, 2024
-
Current status
Jul 10, 2024
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
EMPIAR-10783 (Title: Multi-modal adaptor-clathrin contacts drive coated vesicle assembly Data size: 25.0 Data #1: Hub subparticles of the 28 mini coat, class 15 [picked particles - single frame - processed])
Entire : Beta2 appendage domain of AP2 bound to terminal domains beneath t...
Entire
Name: Beta2 appendage domain of AP2 bound to terminal domains beneath the hub of the 28 triskelia mini clathrin coat complex, class 15
Components
Complex: Beta2 appendage domain of AP2 bound to terminal domains beneath the hub of the 28 triskelia mini clathrin coat complex, class 15
Complex: Clathrin heavy chain
Protein or peptide: Clathrin heavy chain
Complex: AP-2 complex subunit beta
Protein or peptide: AP-2 complex subunit beta
-
Supramolecule #1: Beta2 appendage domain of AP2 bound to terminal domains beneath t...
Supramolecule
Name: Beta2 appendage domain of AP2 bound to terminal domains beneath the hub of the 28 triskelia mini clathrin coat complex, class 15 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Cryogen 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.
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11676
Initial angle assignment
Type: PROJECTION MATCHING
Final angle assignment
Type: PROJECTION MATCHING
FSC plot (resolution estimation)
-
Atomic model buiding 1
Details
This structural model has been updated to include only clathrin terminal domain beta propeller residues that are close to the interface with the beta2 appendage domain.
Output model
PDB-7om8: Beta2 appendage domain of AP2 bound to terminal domains beneath the hub of the 28 triskelia mini clathrin coat complex, class 15
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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