+Open data
-Basic information
Entry | Database: PDB / ID: 7kmi | ||||||
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Title | LY-CoV481 neutralizing antibody against SARS-CoV-2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / antibody neutralizing SARS-CoV-2 / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN 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 / 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 | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Hendle, J. / Pustilnik, A. / Sauder, J.M. / Coleman, K.A. / Boyles, J.S. / Dickinson, C.D. | ||||||
Citation | Journal: Sci Transl Med / Year: 2021 Title: The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates. Authors: Jones, B.E. / Brown-Augsburger, P.L. / Corbett, K.S. / Westendorf, K. / Davies, J. / Cujec, T.P. / Wiethoff, C.M. / Blackbourne, J.L. / Heinz, B.A. / Foster, D. / Higgs, R.E. / ...Authors: Jones, B.E. / Brown-Augsburger, P.L. / Corbett, K.S. / Westendorf, K. / Davies, J. / Cujec, T.P. / Wiethoff, C.M. / Blackbourne, J.L. / Heinz, B.A. / Foster, D. / Higgs, R.E. / Balasubramaniam, D. / Wang, L. / Zhang, Y. / Yang, E.S. / Bidshahri, R. / Kraft, L. / Hwang, Y. / Zentelis, S. / Jepson, K.R. / Goya, R. / Smith, M.A. / Collins, D.W. / Hinshaw, S.J. / Tycho, S.A. / Pellacani, D. / Xiang, P. / Muthuraman, K. / Sobhanifar, S. / Piper, M.H. / Triana, F.J. / Hendle, J. / Pustilnik, A. / Adams, A.C. / Berens, S.J. / Baric, R.S. / Martinez, D.R. / Cross, R.W. / Geisbert, T.W. / Borisevich, V. / Abiona, O. / Belli, H.M. / de Vries, M. / Mohamed, A. / Dittmann, M. / Samanovic, M.I. / Mulligan, M.J. / Goldsmith, J.A. / Hsieh, C.L. / Johnson, N.V. / Wrapp, D. / McLellan, J.S. / Barnhart, B.C. / Graham, B.S. / Mascola, J.R. / Hansen, C.L. / Falconer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kmi.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kmi.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kmi_validation.pdf.gz | 462.9 KB | Display | wwPDB validaton report |
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Full document | 7kmi_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 7kmi_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 7kmi_validation.cif.gz | 42.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/7kmi ftp://data.pdbj.org/pub/pdb/validation_reports/km/7kmi | HTTPS FTP |
-Related structure data
Related structure data | 7kmgSC 7kmhC 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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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23563.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 22939.381 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
-Protein / Sugars , 2 types, 2 molecules C
#3: Protein | Mass: 23173.928 Da / Num. of mol.: 1 / Fragment: receptor-binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2 |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 492 molecules
#4: Chemical | #6: Water | ChemComp-HOH / | |
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-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: 3.27 Å3/Da / Density % sol: 62.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 14% PEG 4000, 10% 2-Propanol, 100 mM Tri-Sodium Citrate pH 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. obs: 93105 / % possible obs: 98.7 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.73→1.83 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 13500 / CC1/2: 0.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KMG Resolution: 1.73→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.291 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.64 Å2 / Biso mean: 28.524 Å2 / Biso min: 12.99 Å2
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Refinement step | Cycle: final / Resolution: 1.73→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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