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- PDB-7mmo: LY-CoV1404 neutralizing antibody against SARS-CoV-2 -

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Basic information

Entry
Database: PDB / ID: 7mmo
TitleLY-CoV1404 neutralizing antibody against SARS-CoV-2
Components
  • LY-CoV1404 Fab heavy chain
  • LY-CoV1404 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 / 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 / symbiont-mediated suppression of host innate immune response / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.427 Å
AuthorsHendle, J. / Pustilnik, A. / Sauder, J.M. / Coleman, K.A. / Boyles, J.S. / Dickinson, C.D.
CitationJournal: Biorxiv / Year: 2022
Title: LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants.
Authors: Westendorf, K. / Wang, L. / Zentelis, S. / Foster, D. / Vaillancourt, P. / Wiggin, M. / Lovett, E. / van der Lee, R. / Hendle, J. / Pustilnik, A. / Sauder, J.M. / Kraft, L. / Hwang, Y. / ...Authors: Westendorf, K. / Wang, L. / Zentelis, S. / Foster, D. / Vaillancourt, P. / Wiggin, M. / Lovett, E. / van der Lee, R. / Hendle, J. / Pustilnik, A. / Sauder, J.M. / Kraft, L. / Hwang, Y. / Siegel, R.W. / Chen, J. / Heinz, B.A. / Higgs, R.E. / Kallewaard, N. / Jepson, K. / Goya, R. / Smith, M.A. / Collins, D.W. / Pellacani, D. / Xiang, P. / de Puyraimond, V. / Ricicova, M. / Devorkin, L. / Pritchard, C. / O'Neill, A. / Dalal, K. / Panwar, P. / Dhupar, H. / Garces, F.A. / Cohen, C. / Dye, J. / Huie, K.E. / Badger, C.V. / Kobasa, D. / Audet, J. / Freitas, J.J. / Hassanali, S. / Hughes, I. / Munoz, L. / Palma, H.C. / Ramamurthy, B. / Cross, R.W. / Geisbert, T.W. / Menacherry, V. / Lokugamage, K. / Borisevich, V. / Lanz, I. / Anderson, L. / Sipahimalani, P. / Corbett, K.S. / Yang, E.S. / Zhang, Y. / Shi, W. / Zhou, T. / Choe, M. / Misasi, J. / Kwong, P.D. / Sullivan, N.J. / Graham, B.S. / Fernandez, T.L. / Hansen, C.L. / Falconer, E. / Mascola, J.R. / Jones, B.E. / Barnhart, B.C.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.title / _citation.year ..._citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LY-CoV1404 Fab heavy chain
B: LY-CoV1404 Fab light chain
C: Spike protein S1
D: LY-CoV1404 Fab heavy chain
E: LY-CoV1404 Fab light chain
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,7907
Polymers140,5696
Non-polymers2211
Water1,29772
1
A: LY-CoV1404 Fab heavy chain
B: LY-CoV1404 Fab light chain
C: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5064
Polymers70,2843
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: LY-CoV1404 Fab heavy chain
E: LY-CoV1404 Fab light chain
F: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)70,2843
Polymers70,2843
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.094, 107.692, 190.472
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody LY-CoV1404 Fab heavy chain


Mass: 24160.293 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-CoV1404 Fab light chain


Mass: 22950.125 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


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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 200mM Trimethylamine N-oxide, 20% PEG MME 2K, 100mM Tris HCl pH 6.0-7.0
PH range: 6.0-7.0

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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 PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.427→94 Å / Num. obs: 57593 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15
Reflection shellResolution: 2.43→2.57 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 9489 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (18-SEP-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KMI

7kmi


Resolution: 2.427→93.75 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.355 / SU Rfree Blow DPI: 0.24 / SU Rfree Cruickshank DPI: 0.245
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 2788 4.85 %RANDOM
Rwork0.2261 ---
obs0.2274 57431 99.5 %-
Displacement parametersBiso max: 124.84 Å2 / Biso mean: 59.22 Å2 / Biso min: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.9924 Å20 Å20 Å2
2---2.5452 Å20 Å2
3---0.5528 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.427→93.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9046 0 14 73 9133
Biso mean--72.25 45.16 -
Num. residues----1217
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2957SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1599HARMONIC5
X-RAY DIFFRACTIONt_it9377HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1278SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6334SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9377HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg12837HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion15.85
LS refinement shellResolution: 2.43→2.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2657 60 5.22 %
Rwork0.2266 1089 -
all0.2285 1149 -
obs--99.91 %

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