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Yorodumi- PDB-7sg4: Structure of SARS-CoV S protein in complex with Receptor Binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sg4 | ||||||
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Title | Structure of SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV Spike Protein Trimer | ||||||
Function / homology | Function and homology information Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å | ||||||
Authors | Gobeil, S. / Acharya, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: A broadly cross-reactive antibody neutralizes and protects against sarbecovirus challenge in mice. Authors: David R Martinez / Alexandra Schäfer / Sophie Gobeil / Dapeng Li / Gabriela De la Cruz / Robert Parks / Xiaozhi Lu / Maggie Barr / Victoria Stalls / Katarzyna Janowska / Esther Beaudoin / ...Authors: David R Martinez / Alexandra Schäfer / Sophie Gobeil / Dapeng Li / Gabriela De la Cruz / Robert Parks / Xiaozhi Lu / Maggie Barr / Victoria Stalls / Katarzyna Janowska / Esther Beaudoin / Kartik Manne / Katayoun Mansouri / Robert J Edwards / Kenneth Cronin / Boyd Yount / Kara Anasti / Stephanie A Montgomery / Juanjie Tang / Hana Golding / Shaunna Shen / Tongqing Zhou / Peter D Kwong / Barney S Graham / John R Mascola / David C Montefiori / S Munir Alam / Gregory Sempowski / Gregory D Sempowski / Surender Khurana / Kevin Wiehe / Kevin O Saunders / Priyamvada Acharya / Barton F Haynes / Ralph S Baric / Abstract: Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus ...Severe acute respiratory syndrome coronaviruses 1 (SARS-CoV) and 2 (SARS-CoV-2), including SARS-CoV-2 variants of concern, can cause deadly infections. The mortality associated with sarbecovirus infection underscores the importance of developing broadly effective countermeasures against them, which could be key in the prevention and mitigation of current and future zoonotic events. Here, we demonstrate the neutralization of SARS-CoV; bat coronaviruses WIV-1 and RsSHC014; and SARS-CoV-2 variants D614G, B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617.1, and B.1.617.2 by a receptor binding domain (RBD)–specific human antibody, DH1047. Prophylactic and therapeutic treatment with DH1047 was protective against SARS-CoV, WIV-1, RsSHC014, and SARS-CoV-2 B.1.351 infection in mice. Binding and structural analysis showed high affinity binding of DH1047 to an epitope that is highly conserved among sarbecoviruses. Thus, DH1047 is a broadly protective antibody that can prevent infection and mitigate outbreaks caused by SARS-related strains and SARS-CoV-2 variants. Our results also suggest that the conserved RBD epitope bound by DH1047 is a rational target for a universal sarbecovirus vaccine. | ||||||
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 | 7sg4.cif.gz | 651.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sg4.ent.gz | 539.9 KB | Display | PDB format |
PDBx/mmJSON format | 7sg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sg4_validation.pdf.gz | 851.8 KB | Display | wwPDB validaton report |
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Full document | 7sg4_full_validation.pdf.gz | 880.9 KB | Display | |
Data in XML | 7sg4_validation.xml.gz | 90.6 KB | Display | |
Data in CIF | 7sg4_validation.cif.gz | 144.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/7sg4 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/7sg4 | HTTPS FTP |
-Related structure data
Related structure data | 25105MC 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: 140644.547 Da / Num. of mol.: 3 / Mutation: K968P, V969P Source method: isolated from a genetically manipulated source Details: C-term Expression tags: GYIPEAPRDGQAYVRKDGEWVLLSTFL = T4 fibritin trimerization motif LEVLFQ = HRV3C protease site HHHHHHHH = His Tag WSHPQFEKGGGSGGGGSGGSAWSHPQFEK = Strep tag Source: (gene. exp.) Severe acute respiratory syndrome coronavirus Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P59594 #2: Antibody | | Mass: 24834.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | | Mass: 24398.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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: SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047 Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Severe acute respiratory syndrome-related coronavirus |
Source (recombinant) | Organism: Homo sapiens (human) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 8 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 54.1 e/Å2 / 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: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284619 / Symmetry type: POINT |