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Yorodumi- EMDB-21608: Mini-coat geometry for a clathrin coated vesicle: clathrin-focused -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21608 | |||||||||
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Title | Mini-coat geometry for a clathrin coated vesicle: clathrin-focused | |||||||||
Map data | Clathrin heavy chain and light chain from natively assembled clathrin coated vesicles, mini-coat geometry. Sharpened and masked. | |||||||||
Sample |
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Biological species | Bos taurus (cattle) / bovine (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.5 Å | |||||||||
Authors | Paraan M / Mendez J / Sharum S / Kurtin D / He H / Stagg S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2020 Title: The structures of natively assembled clathrin-coated vesicles. Authors: Mohammadreza Paraan / Joshua Mendez / Savanna Sharum / Danielle Kurtin / Huan He / Scott M Stagg / Abstract: Clathrin-coated vesicles mediate trafficking of proteins and nutrients in the cell and between organelles. Proteins included in the clathrin-coated vesicles (CCVs) category include clathrin heavy ...Clathrin-coated vesicles mediate trafficking of proteins and nutrients in the cell and between organelles. Proteins included in the clathrin-coated vesicles (CCVs) category include clathrin heavy chain (CHC), clathrin light chain (CLC), and a variety of adaptor protein complexes. Much is known about the structures of the individual CCV components, but data are lacking about the structures of the fully assembled complexes together with membrane and in complex with cargo. Here, we determined the structures of natively assembled CCVs in a variety of geometries. We show that the adaptor β2 appendages crosslink adjacent CHC β-propellers and that the appendage densities are enriched in CCV hexagonal faces. We resolve how adaptor protein 2 and other associated factors in hexagonal faces form an assembly hub with an extensive web of interactions between neighboring β-propellers and propose a structural model that explains how adaptor binding can direct the formation of pentagonal and hexagonal faces. | |||||||||
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_21608.map.gz | 49.7 MB | EMDB map data format | |
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Header (meta data) | emd-21608-v30.xml emd-21608.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21608_fsc.xml | 15.6 KB | Display | FSC data file |
Images | emd_21608.png | 203.8 KB | ||
Masks | emd_21608_msk_1.map | 343 MB | Mask map | |
Others | emd_21608_additional.map.gz emd_21608_half_map_1.map.gz emd_21608_half_map_2.map.gz | 316.9 MB 83.1 MB 83.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21608 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21608 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21608.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Clathrin heavy chain and light chain from natively assembled clathrin coated vesicles, mini-coat geometry. Sharpened and masked. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.646 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_21608_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Clathrin heavy chain and light chain from natively...
File | emd_21608_additional.map | ||||||||||||
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Annotation | Clathrin heavy chain and light chain from natively assembled clathrin coated vesicles, mini-coat geometry. Unmodified. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mini-coat half map
File | emd_21608_half_map_1.map | ||||||||||||
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Annotation | Mini-coat half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Mini-coat half map
File | emd_21608_half_map_2.map | ||||||||||||
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Annotation | Mini-coat half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Natively assembled clathrin coated vesicles
Entire | Name: Natively assembled clathrin coated vesicles |
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Components |
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-Supramolecule #1: Natively assembled clathrin coated vesicles
Supramolecule | Name: Natively assembled clathrin coated vesicles / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bos taurus (cattle) / Organ: brain |
-Macromolecule #1: Clathrin heavy chain
Macromolecule | Name: Clathrin heavy chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: bovine (cattle) |
Sequence | String: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQI FNIEMKSKMK AHTMTDDVTF WKWISLNTVA LVTDNAVYHW SMEGESQPVK MFDRHSSLAG CQIINYRTDA KQKWLLLTGI ...String: MAQILPIRFQ EHLQLQNLGI NPANIGFSTL TMESDKFICI REKVGEQAQV VIIDMNDPSN PIRRPISADS AIMNPASKVI ALKAGKTLQI FNIEMKSKMK AHTMTDDVTF WKWISLNTVA LVTDNAVYHW SMEGESQPVK MFDRHSSLAG CQIINYRTDA KQKWLLLTGI SAQQNRVVGA MQLYSVDRKV SQPIEGHAAS FAQFKMEGNA EESTLFCFAV RGQAGGKLHI IEVGTPPTGN QPFPKKAVDV FFPPEAQNDF PVAMQISEKH DVVFLITKYG YIHLYDLETG TCIYMNRISG ETIFVTAPHE ATAGIIGVNR KGQVLSVCVE EENIIPYITN VLQNPDLALR MAVRNNLAGA EELFARKFNA LFAQGNYSEA AKVAANAPKG ILRTPDTIRR FQSVPAQPGQ TSPLLQYFGI LLDQGQLNKY ESLELCRPVL QQGRKQLLEK WLKEDKLECS EELGDLVKSV DPTLALSVYL RANVPNKVIQ CFAETGQVQK IVLYAKKVGY TPDWIFLLRN VMRISPDQGQ QFAQMLVQDE EPLADITQIV DVFMEYNLIQ QCTAFLLDAL KNNRPSEGPL QTRLLEMNLM HAPQVADAIL GNQMFTHYDR AHIAQLCEKA GLLQRALEHF TDLYDIKRAV VHTHLLNPEW LVNYFGSLSV EDSLECLRAM LSANIRQNLQ ICVQVASKYH EQLSTQSLIE LFESFKSFEG LFYFLGSIVN FSQDPDVHFK YIQAACKTGQ IKEVERICRE SNCYDPERVK NFLKEAKLTD QLPLIIVCDR FDFVHDLVLY LYRNNLQKYI EIYVQKVNPS RLPVVIGGLL DVDCSEDVIK NLILVVRGQF STDELVAEVE KRNRLKLLLP WLEARIHEGC EEPATHNALA KIYIDSNNNP ERFLRENPYY DSRVVGKYCE KRDPHLACVA YERGQCDLEL INVCNENSLF KSLSRYLVRR KDPELWGSVL LESNPYRRPL IDQVVQTALS ETQDPEEVSV TVKAFMTADL PNELIELLEK IVLDNSVFSE HRNLQNLLIL TAIKADRTRV MEYINRLDNY DAPDIANIAI SNELFEEAFA IFRKFDVNTS AVQVLIEHI GNLDRAYEFA ERCNEPAVWS QLAKAQLQKG MVKEAIDSYI KADDPSSYME VVQAANTSGN WEELVKYLQM ARKKARESYV ETELIFALAK TNRLAELEEF INGPNNAHIQ QVGDRCYDEK MYDAAKLLYN NVSNFGRLAS TLVHLGEYQA AVDGARKANS TRTWKEVCFA CVDGKEFRLA QMCGLHIVVH ADELEELINY YQDRGYFEEL ITMLEAALGL ERAHMGMFTE LAILYSKFKP QKMREHLELF WSRVNIPKVL RAAEQAHLWA ELVFLYDKYE EYDNAIITMM NHPTDAWKEG QFKDIITKVA NVELYYRAIQ FYLEFKPLLL NDLLMVLSPR LDHTRAVNYF SKVKQLPLVK PYLRSVQNHN NKSVNESLNN LFITEEDYQA LRTSIDAYDN FDNISLAQRL EKHELIEFRR IAAYLFKGNN RWKQSVELCK KDSLYKDAMQ YASESKDTEL AEELLQWFLQ EEKRECFGAC LFTCYDLLRP DVVLETAWRH NIMDFAMPYF IQVMKEYLTK VDKLDASESL RKEEEQATET QPIVYGQPQL MLTAGPSVAV PPQAPFGYGY TAPAYGQPQP GFGYSM |
-Macromolecule #2: Clathrin light chain
Macromolecule | Name: Clathrin light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: bovine (cattle) |
Sequence | String: MADDFGFFSS SESGAPEAAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QGGLAQPGPA SGASEDMGAT VNGDVFQEAN GPADGYAAIA QADRLTQEPE SIRKWREEQR KRLQELDAAS KVMEQEWREK AKKDLEEWNQ RQSEQVEKNK INNRIADKAF YQQPDADIIG ...String: MADDFGFFSS SESGAPEAAE EDPAAAFLAQ QESEIAGIEN DEGFGAPAGS QGGLAQPGPA SGASEDMGAT VNGDVFQEAN GPADGYAAIA QADRLTQEPE SIRKWREEQR KRLQELDAAS KVMEQEWREK AKKDLEEWNQ RQSEQVEKNK INNRIADKAF YQQPDADIIG YVASEEAFVK ESKEETPGTE WEKVAQLCDF NPKSSKQCKD VSRLRSVLMS LKQTPLSR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL | ||||||||||||
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Buffer | pH: 6.7 Component:
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Grid | Model: 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 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 800 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |