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- PDB-8suo: BA.2/AZD1061/AZD3152 structure analysis -

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Basic information

Entry
Database: PDB / ID: 8suo
TitleBA.2/AZD1061/AZD3152 structure analysis
Components
  • AZD1061 heavy chain
  • AZD1061 light chain
  • AZD3152 heavy chain
  • AZD3152 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / monoclonal antibody / broadly neutralizing / ACE-2 blocking / RBD binding / VIRAL PROTEIN-IMMUNE SYSTEM 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 / 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: 3.3 Å
AuthorsOganesyan, V. / van Dyk, N. / Dippel, A. / Barnes, A. / O'Connor, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: X-ray crystal structure of BA.2 RBD bound by two neutralizing antibodies
Authors: Oganesyan, V. / van Dyk, N. / Dippel, A. / Barnes, A. / O'Connor, E. / Riguero, V. / Taleb, M.
History
DepositionMay 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: AZD1061 heavy chain
M: AZD1061 light chain
H: AZD3152 heavy chain
L: AZD3152 light chain
A: Spike protein S1


Theoretical massNumber of molelcules
Total (without water)117,6425
Polymers117,6425
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-59 kcal/mol
Surface area46580 Å2
Unit cell
Length a, b, c (Å)67.690, 138.000, 188.720
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 AZD1061 heavy chain


Mass: 24834.895 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody AZD1061 light chain


Mass: 24077.725 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody AZD3152 heavy chain


Mass: 24117.016 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody AZD3152 light chain


Mass: 22572.928 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Protein Spike protein S1


Mass: 22039.873 Da / Num. of mol.: 1 / Fragment: receptor-binding domain (UNP residues 333-527) / Source method: isolated from a natural source
Source: (natural) Severe acute respiratory syndrome coronavirus 2
Variant: BA.2 / Strain: Omicron / References: UniProt: P0DTC2

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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: 3.75 Å3/Da / Density % sol: 67.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.12 M D-glucose, 0.12 M D-mannose, 0.12 M D-galactose, 0.12 M L-fructose, 0.12 M D-xylose, 0.12 M N-acetyl-D-glucosamine, 0.1 M Tris, 0.1 M bicine, pH 8.5, 40% v/v ethylene glycol, 20% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97741 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Sep 23, 2022
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.98→94.36 Å / Num. obs: 36925 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 9.5
Reflection shellResolution: 2.98→3.06 Å / Num. unique obs: 2697 / CC1/2: 0.275

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 7L7E, 7UB0, & 7ZFF

7l7e

7ub0

7zff


Resolution: 3.3→30.002 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.842 / WRfactor Rfree: 0.332 / WRfactor Rwork: 0.279 / SU B: 46.281 / SU ML: 0.682 / Average fsc free: 0.8809 / Average fsc work: 0.9126 / Cross valid method: THROUGHOUT / ESU R Free: 0.627
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.332 1376 5.047 %
Rwork0.2789 25889 -
all0.282 --
obs-27265 99.456 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 120.958 Å2
Baniso -1Baniso -2Baniso -3
1--14.157 Å2-0 Å20 Å2
2--16.325 Å20 Å2
3----2.168 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8176 0 0 0 8176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0118384
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167637
X-RAY DIFFRACTIONr_angle_refined_deg0.7771.64511415
X-RAY DIFFRACTIONr_angle_other_deg0.2861.56417671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17751068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.728533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.802101288
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.85610333
X-RAY DIFFRACTIONr_chiral_restr0.0350.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021925
X-RAY DIFFRACTIONr_nbd_refined0.1950.21783
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.28002
X-RAY DIFFRACTIONr_nbtor_refined0.1760.24090
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24341
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.29
X-RAY DIFFRACTIONr_nbd_other0.2010.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.020.23
X-RAY DIFFRACTIONr_mcbond_it4.93212.2094293
X-RAY DIFFRACTIONr_mcbond_other4.93212.2094293
X-RAY DIFFRACTIONr_mcangle_it8.33121.9475354
X-RAY DIFFRACTIONr_mcangle_other8.3321.9495355
X-RAY DIFFRACTIONr_scbond_it4.20212.4164091
X-RAY DIFFRACTIONr_scbond_other4.20212.4174092
X-RAY DIFFRACTIONr_scangle_it7.35722.7746061
X-RAY DIFFRACTIONr_scangle_other7.35622.7746062
X-RAY DIFFRACTIONr_lrange_it16.123146.80734371
X-RAY DIFFRACTIONr_lrange_other16.123146.80634371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.3-3.3850.4431080.43218780.43219950.7780.83799.54890.432
3.385-3.4760.452950.44217980.44218990.7840.84299.6840.442
3.476-3.5760.3891110.39617820.39618960.8420.8699.84180.396
3.576-3.6840.406880.46516680.46217800.7890.82198.65170.465
3.684-3.8030.384870.38316800.38317830.8610.87299.10260.383
3.803-3.9340.423690.39816080.39917090.7440.82298.12760.398
3.934-4.080.269740.28315730.28216470.9350.9391000.283
4.08-4.2430.282920.24415060.24616000.9310.95399.8750.244
4.243-4.4280.298850.22114290.22515150.9370.96399.9340.221
4.428-4.6390.29620.21814090.22114710.950.9641000.218
4.639-4.8830.259650.21313470.21514130.9450.96699.92920.213
4.883-5.1710.241740.20812680.2113420.9610.971000.208
5.171-5.5160.3760.22111840.22612610.9380.96699.92070.221
5.516-5.9420.326500.24511210.24811720.9220.96399.91470.245
5.942-6.4830.295570.25410460.25711040.9410.9699.90940.254
6.483-7.2070.41420.2599590.26410010.90.9551000.259
7.207-8.2430.358450.2258570.2319020.9190.9641000.225
8.243-9.910.332460.2167420.2227880.9190.9691000.216
9.91-13.3080.295300.2266080.2296380.9480.971000.226
13.308-30.0020.382200.3334210.3364410.890.9291000.333

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