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Yorodumi- PDB-7mzj: SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mzj | ||||||
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Title | SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 93 | ||||||
Components |
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Keywords | VIRAL PROTEIN / SARS-CoV-2 / spike / RBD / human 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 / 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 / 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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Pymm, P. / Dietrich, M.H. / Tan, L.L. / Chan, L.J. / Tham, W.H. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Cell Rep / Year: 2021 Title: Landscape of human antibody recognition of the SARS-CoV-2 receptor binding domain. Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon- ...Authors: Adam K Wheatley / Phillip Pymm / Robyn Esterbauer / Melanie H Dietrich / Wen Shi Lee / Damien Drew / Hannah G Kelly / Li-Jin Chan / Francesca L Mordant / Katrina A Black / Amy Adair / Hyon-Xhi Tan / Jennifer A Juno / Kathleen M Wragg / Thakshila Amarasena / Ester Lopez / Kevin J Selva / Ebene R Haycroft / James P Cooney / Hariprasad Venugopal / Li Lynn Tan / Matthew T O Neill / Cody C Allison / Deborah Cromer / Miles P Davenport / Richard A Bowen / Amy W Chung / Marc Pellegrini / Mark T Liddament / Alisa Glukhova / Kanta Subbarao / Stephen J Kent / Wai-Hong Tham / Abstract: Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike ...Potent neutralizing monoclonal antibodies are one of the few agents currently available to treat COVID-19. SARS-CoV-2 variants of concern (VOCs) that carry multiple mutations in the viral spike protein can exhibit neutralization resistance, potentially affecting the effectiveness of some antibody-based therapeutics. Here, the generation of a diverse panel of 91 human, neutralizing monoclonal antibodies provides an in-depth structural and phenotypic definition of receptor binding domain (RBD) antigenic sites on the viral spike. These RBD antibodies ameliorate SARS-CoV-2 infection in mice and hamster models in a dose-dependent manner and in proportion to in vitro, neutralizing potency. Assessing the effect of mutations in the spike protein on antibody recognition and neutralization highlights both potent single antibodies and stereotypic classes of antibodies that are unaffected by currently circulating VOCs, such as B.1.351 and P.1. These neutralizing monoclonal antibodies and others that bind analogous epitopes represent potentially useful future anti-SARS-CoV-2 therapeutics. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mzj.cif.gz | 408.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mzj.ent.gz | 326.6 KB | Display | PDB format |
PDBx/mmJSON format | 7mzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mzj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7mzj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7mzj_validation.xml.gz | 74.1 KB | Display | |
Data in CIF | 7mzj_validation.cif.gz | 102.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/7mzj ftp://data.pdbj.org/pub/pdb/validation_reports/mz/7mzj | HTTPS FTP |
-Related structure data
Related structure data | 7mzfC 7mzgC 7mzhC 7mziSC 7mzkC 7mzlC 7mzmC 7mznC 7rr0C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 4 types, 8 molecules DECFLMHN
#1: Antibody | Mass: 22751.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23568.467 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 23468.033 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #5: Antibody | Mass: 24758.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Protein / Sugars , 2 types, 4 molecules BA
#3: Protein | Mass: 23073.766 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain (RBD) 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 #6: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 2 types, 259 molecules
#7: Chemical | ChemComp-GOL / |
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#8: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 23% PEG3350, 0.1 M sodium acetate pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.953732 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→48.199 Å / Num. obs: 76559 / % possible obs: 98.4 % / Redundancy: 3.636 % / Biso Wilson estimate: 52.713 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.113 / Χ2: 0.849 / Net I/σ(I): 9.28 / Num. measured all: 278333 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7MZI Resolution: 2.4→48.199 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 32.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 238.99 Å2 / Biso mean: 54.644 Å2 / Biso min: 21.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→48.199 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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