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- PDB-7kza: Potent SARS-CoV-2 binding and neutralization through maturation o... -

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Basic information

Entry
Database: PDB / ID: 7kza
TitlePotent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1antibodies
Components(Fab fragment ...) x 2
KeywordsIMMUNE SYSTEM / COVID19 / SARS-CoV2 / antibody / ANTIVIRAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å
AuthorsLangley, D.B. / Christ, D.
CitationJournal: MAbs / Year: 2021
Title: Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1 antibodies.
Authors: Romain Rouet / Ohan Mazigi / Gregory J Walker / David B Langley / Meghna Sobti / Peter Schofield / Helen Lenthall / Jennifer Jackson / Stephanie Ubiparipovic / Jake Y Henry / Arunasingam ...Authors: Romain Rouet / Ohan Mazigi / Gregory J Walker / David B Langley / Meghna Sobti / Peter Schofield / Helen Lenthall / Jennifer Jackson / Stephanie Ubiparipovic / Jake Y Henry / Arunasingam Abayasingam / Deborah Burnett / Anthony Kelleher / Robert Brink / Rowena A Bull / Stuart Turville / Alastair G Stewart / Christopher C Goodnow / William D Rawlinson / Daniel Christ /
Abstract: Antibodies against coronavirus spike protein potently protect against infection and disease, but whether such protection can be extended to variant coronaviruses is unclear. This is exemplified by a ...Antibodies against coronavirus spike protein potently protect against infection and disease, but whether such protection can be extended to variant coronaviruses is unclear. This is exemplified by a set of iconic and well-characterized monoclonal antibodies developed after the 2003 SARS outbreak, including mAbs m396, CR3022, CR3014 and 80R, which potently neutralize SARS-CoV-1, but not SARS-CoV-2. Here, we explore antibody engineering strategies to change and broaden their specificity, enabling nanomolar binding and potent neutralization of SARS-CoV-2. Intriguingly, while many of the matured clones maintained specificity of the parental antibody, new specificities were also observed, which was further confirmed by X-ray crystallography and cryo-electron microscopy, indicating that a limited set of VH antibody domains can give rise to variants targeting diverse epitopes, when paired with a diverse VL repertoire. Our findings open up over 15 years of antibody development efforts against SARS-CoV-1 to the SARS-CoV-2 field and outline general principles for the maturation of antibody specificity against emerging viruses.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
H: Fab fragment heavy chain of anti-CoV2-RBD antibody variant CR3022-B6
L: Fab fragment light chain of anti-CoV2-RBD antibody variant CR3022-B6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,42511
Polymers47,7752
Non-polymers6499
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-62 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.749, 70.749, 249.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11H-401-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab fragment heavy chain of anti-CoV2-RBD antibody variant CR3022-B6


Mass: 24428.432 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) / Strain (production host): ExpiCHO
#2: Antibody Fab fragment light chain of anti-CoV2-RBD antibody variant CR3022-B6


Mass: 23346.889 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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Non-polymers , 5 types, 319 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.27 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.65
Details: Protein (9.6 mg/mL) was mixed with an equal volume (2 uL) of well solution comprising 200 mM sodium citrate (pH 6.65) and 24% (w/v) PEG3350. Cryoprotection was achieved by briefly (5-10 sec) ...Details: Protein (9.6 mg/mL) was mixed with an equal volume (2 uL) of well solution comprising 200 mM sodium citrate (pH 6.65) and 24% (w/v) PEG3350. Cryoprotection was achieved by briefly (5-10 sec) swimming crystals in well solution doped with glycerol to a final concentration of ~25% (v/v), prior to snap freezing.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.69→49.05 Å / Num. obs: 72750 / % possible obs: 99.9 % / Redundancy: 26.6 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.015 / Rrim(I) all: 0.076 / Net I/σ(I): 26.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.69-1.7225.91.5119142235300.8610.2981.5412.697.7
9.08-49.0520.50.0391221959510.0080.0476.499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.57 Å49.05 Å
Translation4.57 Å49.05 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w41

6w41


Resolution: 1.69→49.05 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.015 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0744 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3631 5 %RANDOM
Rwork0.166 ---
obs0.1673 68990 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.79 Å2 / Biso mean: 29.029 Å2 / Biso min: 17.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.62 Å2
Refinement stepCycle: final / Resolution: 1.69→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 38 310 3554
Biso mean--48.07 40.2 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173110
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.644761
X-RAY DIFFRACTIONr_angle_other_deg1.5061.5687296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5025464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1423.968126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08315554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.49158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023933
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02671
LS refinement shellResolution: 1.69→1.729 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.25 249 -
Rwork0.232 4935 -
obs--98.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6956-0.2298-0.19560.510.39160.7664-0.0370.11720.03890.0035-0.04790.0380.067-0.15420.08490.0251-0.02470.0120.0523-0.0110.0191-4.682425.24723.7249
20.6134-0.2514-0.50210.36250.51631.12450.0929-0.04230.1349-0.02220.0326-0.0762-0.06630.1066-0.12560.0429-0.02240.01790.0255-0.01760.049810.614832.494827.7276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 219
2X-RAY DIFFRACTION2L1 - 213

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