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Yorodumi- EMDB-12984: Cryo-EM structure of the hub of the 28 triskelia mini clathrin co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12984 | |||||||||
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Title | Cryo-EM structure of the hub of the 28 triskelia mini clathrin coat complex, class 15 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Clathrin / clathrin adaptor / AP2 / endocytosis | |||||||||
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 | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.5 Å | |||||||||
Authors | Smith SM / Smith CJ | |||||||||
Funding support | United Kingdom, 1 items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12984.map.gz | 9.9 MB | EMDB map data format | |
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Header (meta data) | emd-12984-v30.xml emd-12984.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12984_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_12984.png | 96 KB | ||
Masks | emd_12984_msk_1.map | 163.6 MB | Mask map | |
Filedesc metadata | emd-12984.cif.gz | 6.1 KB | ||
Others | emd_12984_half_map_1.map.gz emd_12984_half_map_2.map.gz | 130.2 MB 130.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12984 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12984 | HTTPS FTP |
-Validation report
Summary document | emd_12984_validation.pdf.gz | 750.8 KB | Display | EMDB validaton report |
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Full document | emd_12984_full_validation.pdf.gz | 750.3 KB | Display | |
Data in XML | emd_12984_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | emd_12984_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12984 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12984 | HTTPS FTP |
-Related structure data
Related structure data | 7om8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | 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]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12984.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12984_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12984_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12984_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-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 |
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Components |
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-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 |
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-Supramolecule #2: Clathrin heavy chain
Supramolecule | Name: Clathrin heavy chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Sus scrofa (pig) |
-Supramolecule #3: AP-2 complex subunit beta
Supramolecule | Name: AP-2 complex subunit beta / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Clathrin heavy chain
Macromolecule | Name: Clathrin heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) |
Molecular weight | Theoretical: 33.535574 KDa |
Sequence | String: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV ALVTDNAVYH WSMEGESQPV KMFDRHSSLA GCQIINYRTD A KQKWLLLT ...String: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQ IFNIEMKSKM KAHTMTDDVT FWKWISLNTV ALVTDNAVYH WSMEGESQPV KMFDRHSSLA GCQIINYRTD A KQKWLLLT GISAQQNRVV GAMQLYSVDR KVSQPIEGHA ASFAQFKMEG NAEESTLFCF AVRGQAGGKL HIIEVGTPPT GN QPFPKKA VDVFFPPEAQ NDFPVAMQIS EKHDVVFLIT KYGYIHLYDL ETGTCIYMNR IS UniProtKB: Clathrin heavy chain |
-Macromolecule #2: AP-2 complex subunit beta
Macromolecule | Name: AP-2 complex subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.429457 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GGYVAPKAVW LPAVKAKGLE ISGTFTHRQG HIYMEMNFTN KALQHMTDFA IQFNKNSFGV IPSTPLAIHT PLMPNQSIDV SLPLNTLGP VMKMEPLNNL QVAVKNNIDV FYFSCLIPLN VLFVEDGKME RQVFLATWKD IPNENELQFQ IKECHLNADT V SSKLQNNN ...String: GGYVAPKAVW LPAVKAKGLE ISGTFTHRQG HIYMEMNFTN KALQHMTDFA IQFNKNSFGV IPSTPLAIHT PLMPNQSIDV SLPLNTLGP VMKMEPLNNL QVAVKNNIDV FYFSCLIPLN VLFVEDGKME RQVFLATWKD IPNENELQFQ IKECHLNADT V SSKLQNNN VYTIAKRNVE GQDMLYQSLK LTNGIWILAE LRIQPGNPNY TLSLKCRAPE VSQYIYQVYD SILKN UniProtKB: AP-2 complex subunit beta |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.4 |
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Vitrification | 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 |
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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 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-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. |
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Output model | PDB-7om8: |