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- PDB-8dw9: Crystal structure of neutralizing antibody D29 Fab in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8dw9
TitleCrystal structure of neutralizing antibody D29 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)
Components
  • D29 Fab light chain
  • D29 Heavy chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SarbecoVirus / WIV1 RBD / Viral protein / Spike glycoprotein / Receptor Binding Protein / Neutralizing antibody / potent / 10-40 / Fab / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / Attachment and Entry / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal ...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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4 Å
AuthorsReddem, E.R. / Shapiro, L.
Funding support China, 1items
OrganizationGrant numberCountry
Jack Ma Foundation China
CitationJournal: Emerg Microbes Infect / Year: 2023
Title: Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2.
Authors: Mengxiao Luo / Biao Zhou / Eswar R Reddem / Bingjie Tang / Bohao Chen / Runhong Zhou / Hang Liu / Lihong Liu / Phinikoula S Katsamba / Ka-Kit Au / Hiu-On Man / Kelvin Kai-Wang To / Kwok-Yung ...Authors: Mengxiao Luo / Biao Zhou / Eswar R Reddem / Bingjie Tang / Bohao Chen / Runhong Zhou / Hang Liu / Lihong Liu / Phinikoula S Katsamba / Ka-Kit Au / Hiu-On Man / Kelvin Kai-Wang To / Kwok-Yung Yuen / Lawrence Shapiro / Shangyu Dang / David D Ho / Zhiwei Chen /
Abstract: Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth ...Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis.
History
DepositionAug 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
C: D29 Heavy chain
D: D29 Fab light chain
H: D29 Heavy chain
L: D29 Fab light chain


Theoretical massNumber of molelcules
Total (without water)135,9506
Polymers135,9506
Non-polymers00
Water00
1
A: Spike protein S1
H: D29 Heavy chain
L: D29 Fab light chain


Theoretical massNumber of molelcules
Total (without water)67,9753
Polymers67,9753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
C: D29 Heavy chain
D: D29 Fab light chain


Theoretical massNumber of molelcules
Total (without water)67,9753
Polymers67,9753
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.171, 106.707, 207.650
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: Protein Spike protein S1


Mass: 21873.496 Da / Num. of mol.: 2 / Fragment: receptor binding domain (UNP residues 333-527)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#2: Antibody D29 Heavy chain


Mass: 23284.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody D29 Fab light chain


Mass: 22817.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 M ammonium sulfate, 0.05 M MES, pH 6.0, 5 mM magnesium acetate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.25→146.18 Å / Num. obs: 15675 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.879 / Rmerge(I) obs: 0.957 / Rpim(I) all: 0.374 / Rrim(I) all: 1.029 / Net I/σ(I): 2.9 / Num. measured all: 416989
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
3.25-3.347.62.6083486746060.2931.0062.7980.899.9
13.79-146.186.90.90452587590.9450.3540.9735.598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXRefinerefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7SD5

7sd5


Resolution: 4→95.09 Å / Cor.coef. Fo:Fc: 0.746 / Cor.coef. Fo:Fc free: 0.683 / SU B: 42 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3807 639 5 %RANDOM
Rwork0.3 ---
obs0.3522 12223 81.98 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.47 Å2 / Biso mean: 40.213 Å2 / Biso min: 41.47 Å2
Baniso -1Baniso -2Baniso -3
1--5.95 Å2-0 Å20 Å2
2--5.08 Å20 Å2
3---0.87 Å2
Refinement stepCycle: final / Resolution: 4→95.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9220 0 0 0 9220
Num. residues----1208
LS refinement shellResolution: 4→4.102 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.359 39 -
Rwork0.35 784 -
obs--72.64 %

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