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- PDB-7raq: Crystal structure of CV3-25 Fab bound to SARS-CoV-2 spike stem he... -

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Basic information

Entry
Database: PDB / ID: 7raq
TitleCrystal structure of CV3-25 Fab bound to SARS-CoV-2 spike stem helix peptide
Components
  • CV3-25 Fab Heavy Chain
  • CV3-25 Fab Light Chain
  • spike stem helix peptide
KeywordsIMMUNE SYSTEM / Antibody / Fab / SARS-CoV-2
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 / Attachment and Entry / membrane fusion / symbiont-mediated suppression of host innate immune response / 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: 1.74 Å
AuthorsHurlburt, N.K. / Pancera, M.
CitationJournal: Commun Biol / Year: 2022
Title: Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit.
Authors: Nicholas K Hurlburt / Leah J Homad / Irika Sinha / Madeleine F Jennewein / Anna J MacCamy / Yu-Hsin Wan / Jim Boonyaratanakornkit / Anton M Sholukh / Abigail M Jackson / Panpan Zhou / Dennis ...Authors: Nicholas K Hurlburt / Leah J Homad / Irika Sinha / Madeleine F Jennewein / Anna J MacCamy / Yu-Hsin Wan / Jim Boonyaratanakornkit / Anton M Sholukh / Abigail M Jackson / Panpan Zhou / Dennis R Burton / Raiees Andrabi / Gabriel Ozorowski / Andrew B Ward / Leonidas Stamatatos / Marie Pancera / Andrew T McGuire /
Abstract: Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread ...Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks could occur. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-CoV protection. We previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 spike, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and binds to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is maintained against the Alpha, Delta, Gamma and Omicron variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region. Negative stain electron microscopy and a 1.74 Å crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs.
History
DepositionJul 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: CV3-25 Fab Heavy Chain
L: CV3-25 Fab Light Chain
P: spike stem helix peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,32112
Polymers50,4843
Non-polymers8379
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-54 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.173, 60.173, 285.825
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11P-1301-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide spike stem helix peptide


Mass: 2239.437 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2

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Antibody , 2 types, 2 molecules HL

#1: Antibody CV3-25 Fab Heavy Chain


Mass: 25026.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)
#2: Antibody CV3-25 Fab Light Chain


Mass: 23218.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293E / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 303 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Na Acetate:HCl, pH 4.5, 2.0M (NH4)2SO4, 0.01M SrCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0092 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0092 Å / Relative weight: 1
ReflectionResolution: 1.74→49.01 Å / Num. obs: 63310 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.025 / Rrim(I) all: 0.035 / Net I/σ(I): 21.7
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
1.74-1.771.90.309662934470.670.3090.4372.7100
9.04-48.961.50.0168715720.9990.0160.02231.699.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.17.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MVZ

5mvz


Resolution: 1.74→49.01 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.274 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 3105 4.9 %RANDOM
Rwork0.1809 ---
obs0.182 60094 99.98 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 93.51 Å2 / Biso mean: 36.109 Å2 / Biso min: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å2-0 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.74→49.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 52 294 3817
Biso mean--58.63 42.33 -
Num. residues----455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0173616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0193302
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.854912
X-RAY DIFFRACTIONr_angle_other_deg1.0432.6927664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66923.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27315571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.811512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02798
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 258 -
Rwork0.361 4315 -
all-4573 -
obs--99.98 %
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)
10.8681-0.0136-0.33390.673-0.03611.3075-0.02390.1995-0.1566-0.2047-0.02170.03180.15260.05340.04560.10050.0215-0.0220.1545-0.03080.0425-0.369-30.07230.169
20.8692-0.10780.12091.4108-0.59212.158-0.0090.02260.00080.0101-0.00040.0152-0.15980.0910.00940.022-0.0059-0.00870.0795-0.0090.01091.089-16.61242.395
39.9359-2.5044-1.8869.9751.17796.0129-0.13370.1065-0.0193-0.33130.20950.1725-0.0670.111-0.07580.2740.0137-0.08410.29660.02690.0325-5.866-17.2752.833
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 215
2X-RAY DIFFRACTION2L1 - 213
3X-RAY DIFFRACTION3P1152 - 1166

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