+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30027 | |||||||||
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Title | the CD9 and EWI-2 complex attached to an anti-CD9 Fab fragment | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information Acrosome Reaction and Sperm:Oocyte Membrane Binding / myoblast fusion involved in skeletal muscle regeneration / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / regulation of macrophage migration / paranodal junction assembly / glial cell migration / platelet alpha granule membrane / negative regulation of platelet aggregation / Uptake and function of diphtheria toxin ...Acrosome Reaction and Sperm:Oocyte Membrane Binding / myoblast fusion involved in skeletal muscle regeneration / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / regulation of macrophage migration / paranodal junction assembly / glial cell migration / platelet alpha granule membrane / negative regulation of platelet aggregation / Uptake and function of diphtheria toxin / cellular response to low-density lipoprotein particle stimulus / clathrin-coated endocytic vesicle membrane / receptor internalization / platelet activation / endocytic vesicle membrane / extracellular vesicle / integrin binding / Platelet degranulation / cell population proliferation / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / focal adhesion / protein-containing complex / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.3 Å | |||||||||
Authors | Umeda R / Satoh Y / Takemoto M / Nakada-Nakura Y / Liu K / Yokoyama T / Shirouzu M / Iwata S / Nomura N / Sato K ...Umeda R / Satoh Y / Takemoto M / Nakada-Nakura Y / Liu K / Yokoyama T / Shirouzu M / Iwata S / Nomura N / Sato K / Ikawa M / Nishizawa T / Nureki O | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Structural insights into tetraspanin CD9 function. Authors: Rie Umeda / Yuhkoh Satouh / Mizuki Takemoto / Yoshiko Nakada-Nakura / Kehong Liu / Takeshi Yokoyama / Mikako Shirouzu / So Iwata / Norimichi Nomura / Ken Sato / Masahito Ikawa / Tomohiro ...Authors: Rie Umeda / Yuhkoh Satouh / Mizuki Takemoto / Yoshiko Nakada-Nakura / Kehong Liu / Takeshi Yokoyama / Mikako Shirouzu / So Iwata / Norimichi Nomura / Ken Sato / Masahito Ikawa / Tomohiro Nishizawa / Osamu Nureki / Abstract: Tetraspanins play critical roles in various physiological processes, ranging from cell adhesion to virus infection. The members of the tetraspanin family have four membrane-spanning domains and short ...Tetraspanins play critical roles in various physiological processes, ranging from cell adhesion to virus infection. The members of the tetraspanin family have four membrane-spanning domains and short and large extracellular loops, and associate with a broad range of other functional proteins to exert cellular functions. Here we report the crystal structure of CD9 and the cryo-electron microscopic structure of CD9 in complex with its single membrane-spanning partner protein, EWI-2. The reversed cone-like molecular shape of CD9 generates membrane curvature in the crystalline lipid layers, which explains the CD9 localization in regions with high membrane curvature and its implications in membrane remodeling. The molecular interaction between CD9 and EWI-2 is mainly mediated through the small residues in the transmembrane region and protein/lipid interactions, whereas the fertilization assay revealed the critical involvement of the LEL region in the sperm-egg fusion, indicating the different dependency of each binding domain for other partner proteins. | |||||||||
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_30027.map.gz | 4.6 MB | EMDB map data format | |
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Header (meta data) | emd-30027-v30.xml emd-30027.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30027_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_30027.png | 46.3 KB | ||
Others | emd_30027_half_map_1.map.gz emd_30027_half_map_2.map.gz | 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30027 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30027 | HTTPS FTP |
-Validation report
Summary document | emd_30027_validation.pdf.gz | 445.8 KB | Display | EMDB validaton report |
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Full document | emd_30027_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | emd_30027_validation.xml.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30027 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30027 | HTTPS FTP |
-Related structure data
Related structure data | 6k4jMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30027.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.352 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_30027_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30027_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : the complex of CD9 and EWI-2, attached to a Fab fragment
Entire | Name: the complex of CD9 and EWI-2, attached to a Fab fragment |
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Components |
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-Supramolecule #1: the complex of CD9 and EWI-2, attached to a Fab fragment
Supramolecule | Name: the complex of CD9 and EWI-2, attached to a Fab fragment type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293S Gnt1(-) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |