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Yorodumi- PDB-7dzx: Spike protein from SARS-CoV2 with Fab fragment of enhancing antib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dzx | ||||||||||||||||||||||||
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Title | Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 8D2 | ||||||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV2 / spike protein / Fab / enhancing antibody | ||||||||||||||||||||||||
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 Homo sapiens (human) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å | ||||||||||||||||||||||||
Authors | Liu, Y. / Soh, W.T. / Li, S. / Kishikawa, J. / Hirose, M. / Kato, T. / Standley, D. / Okada, M. / Arase, H. | ||||||||||||||||||||||||
Funding support | Japan, 7items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7dzx.cif.gz | 486.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dzx.ent.gz | 284.2 KB | Display | PDB format |
PDBx/mmJSON format | 7dzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dzx_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7dzx_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7dzx_validation.xml.gz | 94.2 KB | Display | |
Data in CIF | 7dzx_validation.cif.gz | 153.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/7dzx ftp://data.pdbj.org/pub/pdb/validation_reports/dz/7dzx | HTTPS FTP |
-Related structure data
Related structure data | 30918MC 7dzwC 7dzyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 138320.891 Da / Num. of mol.: 3 / Mutation: D614G, R682G, R683S, R685G, K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | | Mass: 24330.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) #3: Antibody | | Mass: 23194.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 0.059 mm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2135 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 169524 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building | Source name: PDB / Type: experimental model
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