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- PDB-7kmg: LY-CoV555 neutralizing antibody against SARS-CoV-2 -

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Basic information

Entry
Database: PDB / ID: 7kmg
TitleLY-CoV555 neutralizing antibody against SARS-CoV-2
Components
  • LY-CoV555 Fab heavy chain
  • LY-CoV555 Fab light chain
  • Spike protein S1
KeywordsIMMUNE 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 / identical protein binding / membrane / plasma membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsHendle, J. / Pustilnik, A. / Sauder, J.M. / Coleman, K.A. / Boyles, J.S. / Dickinson, C.D.
CitationJournal: 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
DepositionNov 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LY-CoV555 Fab heavy chain
B: LY-CoV555 Fab light chain
C: Spike protein S1
D: LY-CoV555 Fab heavy chain
E: LY-CoV555 Fab light chain
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3438
Polymers142,1596
Non-polymers1842
Water3,549197
1
A: LY-CoV555 Fab heavy chain
B: LY-CoV555 Fab light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1714
Polymers71,0793
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-36 kcal/mol
Surface area27580 Å2
MethodPISA
2
D: LY-CoV555 Fab heavy chain
E: LY-CoV555 Fab light chain
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1714
Polymers71,0793
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-39 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.317, 280.364, 68.909
Angle α, β, γ (deg.)90.000, 99.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody LY-CoV555 Fab heavy chain


Mass: 24807.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody LY-CoV555 Fab light chain


Mass: 23097.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 23173.928 Da / Num. of mol.: 2 / 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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 20% PEG 10000, sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.16→30 Å / Num. obs: 77441 / % possible obs: 91.2 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 6.2
Reflection shellResolution: 2.16→2.29 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9083 / CC1/2: 0.82 / % possible all: 82.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YLA

6yla


Resolution: 2.16→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.895 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 3756 4.9 %RANDOM
Rwork0.2086 ---
obs0.211 73545 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.32 Å2 / Biso mean: 43.404 Å2 / Biso min: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å2-2.46 Å2
2---1.09 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.16→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9360 0 12 201 9573
Biso mean--33.66 38.37 -
Num. residues----1255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0129671
X-RAY DIFFRACTIONr_angle_refined_deg1.021.6413206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98451269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21923.848382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9531539
X-RAY DIFFRACTIONr_chiral_restr0.0840.21305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027355
LS refinement shellResolution: 2.16→2.216 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 245 -
Rwork0.299 4979 -
all-5224 -
obs--83.22 %

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