+Open data
-Basic information
Entry | Database: PDB / ID: 7kmh | ||||||
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Title | LY-CoV488 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Hendle, J. / Pustilnik, A. / Sauder, J.M. / Boyles, J.S. / Dickinson, C.D. / Coleman, K.A. | ||||||
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 | 7kmh.cif.gz | 258.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kmh.ent.gz | 203.8 KB | Display | PDB format |
PDBx/mmJSON format | 7kmh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/7kmh ftp://data.pdbj.org/pub/pdb/validation_reports/km/7kmh | HTTPS FTP |
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-Related structure data
Related structure data | 7kmgSC 7kmiC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23298.967 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: 23287.666 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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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 262 molecules
#5: Chemical | ChemComp-GOL / |
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#6: Chemical | ChemComp-PRO / |
#7: 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: 3.32 Å3/Da / Density % sol: 62.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 8% PEG 3350, 200 mM L-Proline, 100 mM Hepes pH 7.7 |
-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: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→30 Å / Num. obs: 97212 / % possible obs: 98.8 % / Redundancy: 13 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.72→1.82 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 14015 / CC1/2: 0.973 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7KMG Resolution: 1.72→29.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.531 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / ESU R Free: 0.021 / 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: 140.4 Å2 / Biso mean: 40.618 Å2 / Biso min: 13.53 Å2
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Refinement step | Cycle: final / Resolution: 1.72→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.764 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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