+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30915 | ||||||||||||||||||||||||
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Title | Apo spike protein of SARS-CoV2 | ||||||||||||||||||||||||
Map data | Apo spike protein of SARS-CoV2 | ||||||||||||||||||||||||
Sample |
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Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | ||||||||||||||||||||||||
Authors | Liu Y / Soh WT / Kishikawa J / Hirose M / Kato T / Okada M / Arase H | ||||||||||||||||||||||||
Funding support | Japan, 7 items
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Citation | Journal: Cell / Year: 2021 Title: An infectivity-enhancing site on the SARS-CoV-2 spike protein targeted by antibodies. Authors: Yafei Liu / Wai Tuck Soh / Jun-Ichi Kishikawa / Mika Hirose / Emi E Nakayama / Songling Li / Miwa Sasai / Tatsuya Suzuki / Asa Tada / Akemi Arakawa / Sumiko Matsuoka / Kanako Akamatsu / ...Authors: Yafei Liu / Wai Tuck Soh / Jun-Ichi Kishikawa / Mika Hirose / Emi E Nakayama / Songling Li / Miwa Sasai / Tatsuya Suzuki / Asa Tada / Akemi Arakawa / Sumiko Matsuoka / Kanako Akamatsu / Makoto Matsuda / Chikako Ono / Shiho Torii / Kazuki Kishida / Hui Jin / Wataru Nakai / Noriko Arase / Atsushi Nakagawa / Maki Matsumoto / Yukoh Nakazaki / Yasuhiro Shindo / Masako Kohyama / Keisuke Tomii / Koichiro Ohmura / Shiro Ohshima / Toru Okamoto / Masahiro Yamamoto / Hironori Nakagami / Yoshiharu Matsuura / Atsushi Nakagawa / Takayuki Kato / Masato Okada / Daron M Standley / Tatsuo Shioda / Hisashi Arase / Abstract: Antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein prevent SARS-CoV-2 infection. However, the effects of antibodies against other spike protein domains are largely ...Antibodies against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein prevent SARS-CoV-2 infection. However, the effects of antibodies against other spike protein domains are largely unknown. Here, we screened a series of anti-spike monoclonal antibodies from coronavirus disease 2019 (COVID-19) patients and found that some of antibodies against the N-terminal domain (NTD) induced the open conformation of RBD and thus enhanced the binding capacity of the spike protein to ACE2 and infectivity of SARS-CoV-2. Mutational analysis revealed that all of the infectivity-enhancing antibodies recognized a specific site on the NTD. Structural analysis demonstrated that all infectivity-enhancing antibodies bound to NTD in a similar manner. The antibodies against this infectivity-enhancing site were detected at high levels in severe patients. Moreover, we identified antibodies against the infectivity-enhancing site in uninfected donors, albeit at a lower frequency. These findings demonstrate that not only neutralizing antibodies but also enhancing antibodies are produced during SARS-CoV-2 infection. | ||||||||||||||||||||||||
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_30915.map.gz | 88.8 MB | EMDB map data format | |
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Header (meta data) | emd-30915-v30.xml emd-30915.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30915_fsc.xml | 12.5 KB | Display | FSC data file |
Images | emd_30915.png | 101.4 KB | ||
Masks | emd_30915_msk_1.map | 178 MB | Mask map | |
Others | emd_30915_half_map_1.map.gz emd_30915_half_map_2.map.gz | 165.3 MB 165.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30915 | HTTPS FTP |
-Validation report
Summary document | emd_30915_validation.pdf.gz | 693.1 KB | Display | EMDB validaton report |
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Full document | emd_30915_full_validation.pdf.gz | 692.6 KB | Display | |
Data in XML | emd_30915_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | emd_30915_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30915 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30915 | HTTPS FTP |
-Related structure data
Related structure data | 7dzwMC 7dzxC 7dzyC M: atomic model generated by this map C: citing same article (ref.) |
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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_30915.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Apo spike protein of SARS-CoV2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 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_30915_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Apo spike protein of SARS-CoV2, half map A
File | emd_30915_half_map_1.map | ||||||||||||
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Annotation | Apo spike protein of SARS-CoV2, half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Apo spike protein of SARS-CoV2, half map B
File | emd_30915_half_map_2.map | ||||||||||||
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Annotation | Apo spike protein of SARS-CoV2, half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Apo spike protein trimer of SARS-CoV2
Entire | Name: Apo spike protein trimer of SARS-CoV2 |
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Components |
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-Supramolecule #1: Apo spike protein trimer of SARS-CoV2
Supramolecule | Name: Apo spike protein trimer of SARS-CoV2 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: Expi293F |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0452 mm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |