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- PDB-8dao: Crystal structure of SARS-CoV-2 spike stem fusion peptide in comp... -

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Basic information

Entry
Database: PDB / ID: 8dao
TitleCrystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79
Components
  • COV44-79 heavy chain constant domain
  • COV44-79 heavy chain variable domain
  • COV44-79 light chain constant domain
  • COV44-79 light chain variable domain
  • Spike protein S2 fusion peptide
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / coronavirus / antibody / fusion peptide / neutralizing antibody / COVID-19
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / symbiont-mediated disruption of host tissue / blood microparticle / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / adaptive immune response / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / 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 / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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. / 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 S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin gamma-1 heavy chain / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLin, T.H. / Lee, C.C.D. / Yuan, M. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: Science / Year: 2022
Title: Broadly neutralizing antibodies target the coronavirus fusion peptide.
Authors: Dacon, C. / Tucker, C. / Peng, L. / Lee, C.D. / Lin, T.H. / Yuan, M. / Cong, Y. / Wang, L. / Purser, L. / Williams, J.K. / Pyo, C.W. / Kosik, I. / Hu, Z. / Zhao, M. / Mohan, D. / Cooper, A.J. ...Authors: Dacon, C. / Tucker, C. / Peng, L. / Lee, C.D. / Lin, T.H. / Yuan, M. / Cong, Y. / Wang, L. / Purser, L. / Williams, J.K. / Pyo, C.W. / Kosik, I. / Hu, Z. / Zhao, M. / Mohan, D. / Cooper, A.J.R. / Peterson, M. / Skinner, J. / Dixit, S. / Kollins, E. / Huzella, L. / Perry, D. / Byrum, R. / Lembirik, S. / Drawbaugh, D. / Eaton, B. / Zhang, Y. / Yang, E.S. / Chen, M. / Leung, K. / Weinberg, R.S. / Pegu, A. / Geraghty, D.E. / Davidson, E. / Douagi, I. / Moir, S. / Yewdell, J.W. / Schmaljohn, C. / Crompton, P.D. / Holbrook, M.R. / Nemazee, D. / Mascola, J.R. / Wilson, I.A. / Tan, J.
History
DepositionJun 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 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
C: COV44-79 heavy chain variable domain
D: COV44-79 light chain variable domain
E: COV44-79 heavy chain constant domain
F: COV44-79 light chain constant domain
I: Spike protein S2 fusion peptide
A: COV44-79 heavy chain variable domain
B: COV44-79 light chain variable domain
G: COV44-79 heavy chain constant domain
H: COV44-79 light chain constant domain
J: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)99,47610
Polymers99,47610
Non-polymers00
Water00
1
C: COV44-79 heavy chain variable domain
D: COV44-79 light chain variable domain
E: COV44-79 heavy chain constant domain
F: COV44-79 light chain constant domain
I: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)49,7385
Polymers49,7385
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: COV44-79 heavy chain variable domain
B: COV44-79 light chain variable domain
G: COV44-79 heavy chain constant domain
H: COV44-79 light chain constant domain
J: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)49,7385
Polymers49,7385
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.368, 100.368, 229.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Antibody COV44-79 heavy chain variable domain


Mass: 13673.513 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#2: Antibody COV44-79 light chain variable domain


Mass: 11933.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Protein COV44-79 heavy chain constant domain / Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 10585.920 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: P0DOX5
#4: Protein COV44-79 light chain constant domain / Immunoglobulin kappa constant / Ig kappa chain C region / Ig kappa chain C region AG / Ig kappa ...Immunoglobulin kappa constant / Ig kappa chain C region / Ig kappa chain C region AG / Ig kappa chain C region CUM / Ig kappa chain C region EU / Ig kappa chain C region OU / Ig kappa chain C region ROY / Ig kappa chain C region TI


Mass: 11778.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKC / Production host: Mus musculus (house mouse) / References: UniProt: P01834
#5: Protein/peptide Spike protein S2 fusion peptide


Mass: 1767.054 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
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: 2.91 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.01 M nickel (II) chloride, and 20% PEG monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 29592 / % possible obs: 98.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 63.87 Å2 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.056 / Rrim(I) all: 0.188 / Χ2: 0.421 / Net I/σ(I): 2.9 / Num. measured all: 309440
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.859.91.4113840.4060.4391.4820.21495.9
2.85-2.910.11.2814020.520.3971.3450.21796
2.9-2.96101.17814210.5480.3661.2380.2395.1
2.96-3.02100.94713840.6810.2940.9950.23397.5
3.02-3.089.80.8114500.7740.2560.8530.24197.8
3.08-3.159.90.67514490.8210.2140.7110.25497.8
3.15-3.239.90.58814460.8560.1880.620.27699.1
3.23-3.32100.48414610.9030.1550.510.28999.4
3.32-3.429.90.39714640.9670.1290.4190.31599.8
3.42-3.539.80.31814750.9550.1040.3360.34799.9
3.53-3.659.60.26314930.9720.0870.2780.3699.8
3.65-3.88.70.23414680.9760.0830.2490.39899.8
3.8-3.979.10.19414900.9820.0670.2060.40999.5
3.97-4.1811.50.15515050.9930.0470.1620.443100
4.18-4.44120.12814820.9940.0390.1340.516100
4.44-4.7912.10.11415220.9960.0340.1190.546100
4.79-5.2712.10.10615160.9960.0310.1110.549100
5.27-6.0311.80.1115240.9950.0330.1150.5299.8
6.03-7.5910.30.09615550.9960.0310.1010.56299.6
7.59-5012.10.06417010.9990.0190.0671.036100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8D6Z

8d6z


Resolution: 2.8→49.88 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2837 1457 4.94 %
Rwork0.2306 28040 -
obs0.2332 29497 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.5 Å2 / Biso mean: 65.5669 Å2 / Biso min: 4.9 Å2
Refinement stepCycle: final / Resolution: 2.8→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 0 0 6914
Num. residues----912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.90.35711310.30042596272793
2.9-3.010.3341250.29852664278996
3.01-3.150.42841610.31152741290298
3.15-3.310.35031490.29512754290399
3.32-3.520.32481520.25427932945100
3.52-3.790.38861290.251528342963100
3.79-4.180.25811440.215328502994100
4.18-4.780.20331410.178828673008100
4.78-6.020.25521610.188528753036100
6.02-49.880.23721640.227630663230100

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