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Yorodumi- PDB-8h3n: Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein c... -
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-Basic information
Entry | Database: PDB / ID: 8h3n | ||||||
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Title | Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 | ||||||
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 / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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: 2.73 Å | ||||||
Authors | Ishimaru, H. / Nishimura, M. / Sutandhio, S. / Shigematsu, H. / Kato, K. / Hasegawa, N. / Mori, Y. | ||||||
Funding support | 1items
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Citation | Journal: J Virol / Year: 2023 Title: Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants. Authors: Hanako Ishimaru / Mitsuhiro Nishimura / Lidya Handayani Tjan / Silvia Sutandhio / Maria Istiqomah Marini / Gema Barlian Effendi / Hideki Shigematsu / Koji Kato / Natsumi Hasegawa / Kaito ...Authors: Hanako Ishimaru / Mitsuhiro Nishimura / Lidya Handayani Tjan / Silvia Sutandhio / Maria Istiqomah Marini / Gema Barlian Effendi / Hideki Shigematsu / Koji Kato / Natsumi Hasegawa / Kaito Aoki / Yukiya Kurahashi / Koichi Furukawa / Mai Shinohara / Tomoka Nakamura / Jun Arii / Tatsuya Nagano / Sachiko Nakamura / Shigeru Sano / Sachiyo Iwata / Shinya Okamura / Yasuko Mori / Abstract: We identified neutralizing monoclonal antibodies against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants (including Omicron variants BA.5 and BA.2.75) from individuals who ...We identified neutralizing monoclonal antibodies against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants (including Omicron variants BA.5 and BA.2.75) from individuals who received two doses of mRNA vaccination after they had been infected with the D614G virus. We named them MO1, MO2, and MO3. Among them, MO1 showed particularly high neutralizing activity against authentic variants: D614G, Delta, BA.1, BA.1.1, BA.2, BA.2.75, and BA.5. Furthermore, MO1 suppressed BA.5 infection in hamsters. A structural analysis revealed that MO1 binds to the conserved epitope of seven variants, including Omicron variants BA.5 and BA.2.75, in the receptor-binding domain of the spike protein. MO1 targets an epitope conserved among Omicron variants BA.1, BA.2, and BA.5 in a unique binding mode. Our findings confirm that D614G-derived vaccination can induce neutralizing antibodies that recognize the epitopes conserved among the SARS-CoV-2 variants. Omicron variants of SARS-CoV-2 acquired escape ability from host immunity and authorized antibody therapeutics and thereby have been spreading worldwide. We reported that patients infected with an early SARS-CoV-2 variant, D614G, and who received subsequent two-dose mRNA vaccination have high neutralizing antibody titer against Omicron lineages. It was speculated that the patients have neutralizing antibodies broadly effective against SARS-CoV-2 variants by targeting common epitopes. Here, we explored human monoclonal antibodies from B cells of the patients. One of the monoclonal antibodies, named MO1, showed high potency against broad SARS-CoV-2 variants including BA.2.75 and BA.5 variants. The results prove that monoclonal antibodies that have common neutralizing epitopes among several Omicrons were produced in patients infected with D614G and who received mRNA vaccination. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h3n.cif.gz | 685.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h3n.ent.gz | 539.2 KB | Display | PDB format |
PDBx/mmJSON format | 8h3n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h3n_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8h3n_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8h3n_validation.xml.gz | 103.7 KB | Display | |
Data in CIF | 8h3n_validation.cif.gz | 159.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/8h3n ftp://data.pdbj.org/pub/pdb/validation_reports/h3/8h3n | HTTPS FTP |
-Related structure data
Related structure data | 34470MC 8h3mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 139267.922 Da / Num. of mol.: 3 Mutation: D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, ...Mutation: D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Plasmid: pCAGGS / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #2: Antibody | Mass: 48630.184 Da / Num. of mol.: 2 / Mutation: ins52A, ins100PGYFLNSF Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSEss-CHIg-hG1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) #3: Antibody | Mass: 23433.045 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFUSE2ss-CLIg-hK / Cell line (production host): HEK293T / Production host: Homo sapiens (human) #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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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 | Name: Spike protein complexed with MO1 Fab / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 0.5 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 | ||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 8 | ||||||||||||
Buffer component |
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Specimen | Conc.: 9.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226284 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |