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

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Basic information

Entry
Database: PDB / ID: 7kzc
TitlePotent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1antibodies
Components
  • Fab heavy chain of m396-B10 antibody
  • Fab light chain of m396-B10 antibody
KeywordsIMMUNE SYSTEM / COVID19 / SARS-CoV2 / antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab heavy chain of m396-B10 antibody
L: Fab light chain of m396-B10 antibody
C: Fab heavy chain of m396-B10 antibody
D: Fab light chain of m396-B10 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9686
Polymers92,8974
Non-polymers712
Water1,76598
1
H: Fab heavy chain of m396-B10 antibody
L: Fab light chain of m396-B10 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5194
Polymers46,4482
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-38 kcal/mol
Surface area19690 Å2
MethodPISA
2
C: Fab heavy chain of m396-B10 antibody
D: Fab light chain of m396-B10 antibody


Theoretical massNumber of molelcules
Total (without water)46,4482
Polymers46,4482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-24 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.311, 68.311, 188.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody Fab heavy chain of m396-B10 antibody


Mass: 23079.701 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 Fab light chain of m396-B10 antibody


Mass: 23368.664 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.36 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.95
Details: Protein was combined with equal volume of well solution comprising 200 mM NaCl, 100 mM BisTris (pH 5.95) and 25% (w/v) PEG3350

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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: 2.3→48.3 Å / Num. obs: 38056 / % possible obs: 99.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.058 / Rrim(I) all: 0.219 / Net I/σ(I): 9.9
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
2.3-2.3814.11.4515125736360.6920.3961.505297.7
8.91-48.313.50.07992436870.9930.0220.08227.599.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.06 Å48.3 Å
Translation3.06 Å48.3 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: 5wl2

5wl2


Resolution: 2.3→48.3 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 18.465 / SU ML: 0.21 / SU R Cruickshank DPI: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1957 5.2 %RANDOM
Rwork0.2119 ---
obs0.2143 36041 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.44 Å2 / Biso mean: 32.413 Å2 / Biso min: 17.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.07 Å2
Refinement stepCycle: final / Resolution: 2.3→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 2 98 6180
Biso mean--46.75 28.38 -
Num. residues----825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136255
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175493
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6468548
X-RAY DIFFRACTIONr_angle_other_deg1.2371.57212811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg18.7035.371850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79123.416243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.38215913
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4351521
X-RAY DIFFRACTIONr_chiral_restr0.0650.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021222
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 137 -
Rwork0.286 2570 -
all-2707 -
obs--96.82 %
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)
12.16750.68790.42181.02250.24080.84180.0148-0.13620.10730.0251-0.03340.00310.08190.03120.01850.0520.01940.01830.01770.00020.0298-8.975713.599912.1415
21.60430.44480.09620.9985-0.0750.3688-0.02450.07150.0459-0.1351-0.021-0.0632-0.0559-0.0170.04550.06040.00620.0290.0076-0.00050.0343-11.221821.5222-3.317
31.5619-0.91530.48491.9202-0.15210.6784-0.00410.1093-0.0909-0.0693-0.01130.18890.06130.03150.01540.033-0.0239-0.00560.02960.00110.041718.9355-20.74021.5261
42.1051-0.48960.07650.8774-0.08020.11210.0115-0.08680.01860.11290.00260.0818-0.05030.0308-0.01420.0479-0.0120.02550.0153-0.00220.022821.1753-12.601717.0213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 220
2X-RAY DIFFRACTION2L1 - 215
3X-RAY DIFFRACTION3C1 - 219
4X-RAY DIFFRACTION4D1 - 213

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