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Yorodumi- PDB-7tcc: Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with ant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tcc | ||||||
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Title | Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibodies A19-46.1 and B1-182.1 | ||||||
Components |
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Keywords | VIRAL PROTEIN/Immune System / SARS-CoV-2 / spike / antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | ||||||
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 / membrane fusion / 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: 3.86 Å | ||||||
Authors | Zhou, T. / Kwong, P.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2022 Title: Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng ...Authors: Tongqing Zhou / Lingshu Wang / John Misasi / Amarendra Pegu / Yi Zhang / Darcy R Harris / Adam S Olia / Chloe Adrienna Talana / Eun Sung Yang / Man Chen / Misook Choe / Wei Shi / I-Ting Teng / Adrian Creanga / Claudia Jenkins / Kwanyee Leung / Tracy Liu / Erik-Stephane D Stancofski / Tyler Stephens / Baoshan Zhang / Yaroslav Tsybovsky / Barney S Graham / John R Mascola / Nancy J Sullivan / Peter D Kwong / Abstract: The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a ...The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tcc.cif.gz | 833.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tcc.ent.gz | 686.1 KB | Display | PDB format |
PDBx/mmJSON format | 7tcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tcc_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7tcc_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7tcc_validation.xml.gz | 141.3 KB | Display | |
Data in CIF | 7tcc_validation.cif.gz | 214.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/7tcc ftp://data.pdbj.org/pub/pdb/validation_reports/tc/7tcc | HTTPS FTP |
-Related structure data
Related structure data | 25808MC 7tb8C 7tbfC 7tc9C 7tcaC 7u0dC 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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1 |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 141111.234 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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-Antibody , 4 types, 12 molecules DHMELNJOFKPG
#2: Antibody | Mass: 14057.687 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 11473.737 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 13473.101 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #5: Antibody | Mass: 11775.985 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 2 types, 28 molecules
#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Details
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-2 spike in complex with antibodies B1-182.1 and A19-46.1 Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT |
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Molecular weight | Value: 0.570 MDa / Experimental value: NO |
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 / Details: 100 mM HEPES, 150 mM NaCl |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Complex at 0.5 mg/mL concentration in the buffer |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: Blot for 2-3.5 seconds before plugging. |
-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 / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: OTHER |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.86 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 46244 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7MM0 | ||||||||||||||||||||||||
Refine LS restraints |
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