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- PDB-8d36: Crystal structure of SARS-CoV-2 fusion peptide in complex with ne... -

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Basic information

Entry
Database: PDB / ID: 8d36
TitleCrystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody COV44-62
Components
  • Neutralizing antibody COV44-62 heavy chain
  • Neutralizing antibody COV44-62 light chain
  • Spike protein S2 fusion peptide
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / coronavirus / antibody / fusion peptide / neutralizing antibody / COVID-19
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 / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / 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 / 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 / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYuan, M. / Lee, C.C.D. / 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
DepositionMay 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
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
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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Neutralizing antibody COV44-62 heavy chain
L: Neutralizing antibody COV44-62 light chain
F: Spike protein S2 fusion peptide


Theoretical massNumber of molelcules
Total (without water)48,6893
Polymers48,6893
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-28 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.535, 71.915, 76.258
Angle α, β, γ (deg.)90.000, 114.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-921-

HOH

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Components

#1: Antibody Neutralizing antibody COV44-62 heavy chain


Mass: 24216.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#2: Antibody Neutralizing antibody COV44-62 light chain


Mass: 22676.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Protein/peptide Spike protein S2 fusion peptide


Mass: 1796.095 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M sodium citrate, pH 4, 1 M lithium chloride, and 10% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 80350 / % possible obs: 93.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 17.43 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.031 / Rrim(I) all: 0.075 / Χ2: 1.293 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.46-1.494.30.74327830.7670.360.8290.42165
1.49-1.514.80.6232020.8470.2870.6850.44474.8
1.51-1.544.80.5834510.8570.2670.640.46580.5
1.54-1.574.90.50337930.9090.230.5550.47288.7
1.57-1.615.10.43440690.9330.1960.4780.4895.2
1.61-1.645.30.3741710.950.1680.4080.50597.4
1.64-1.695.50.32342050.960.1460.3550.53198.1
1.69-1.735.60.27541710.9690.1240.3030.57298
1.73-1.785.40.22440990.9780.1040.2480.65795.5
1.78-1.845.60.18841550.9850.0860.2080.73196.9
1.84-1.916.10.15942570.9890.0690.1740.88499.2
1.91-1.986.10.13642570.9910.0590.1481.09499
1.98-2.0760.11442490.9930.050.1251.25999.1
2.07-2.1860.09942500.9940.0440.1091.47198.7
2.18-2.325.90.08742070.9940.0390.0961.70398.5
2.32-2.55.50.07541630.9950.0350.0831.83495.9
2.5-2.755.90.06741080.9960.030.0732.12396.3
2.75-3.1560.05642250.9980.0250.0622.51897.2
3.15-3.965.90.04842530.9980.0210.0532.92398.5
3.96-505.80.04342820.9970.0190.0472.96996.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 1.45→39.2 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 4003 4.98 %
Rwork0.1965 76319 -
obs0.1976 80322 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.45 Å2 / Biso mean: 27.1469 Å2 / Biso min: 10.73 Å2
Refinement stepCycle: final / Resolution: 1.45→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 0 525 3848
Biso mean---37.81 -
Num. residues----444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.470.3097810.32841743182461
1.47-1.490.34221050.30242001210671
1.49-1.510.29091250.28962104222976
1.51-1.530.35771240.29242221234579
1.53-1.550.32031350.2932386252185
1.55-1.570.32381300.30282547267790
1.57-1.590.35651340.29832638277295
1.59-1.620.28281520.28842732288497
1.62-1.650.26781480.26522726287498
1.65-1.670.30031540.25132744289898
1.67-1.70.23891470.23472779292698
1.7-1.740.25431360.22672727286398
1.74-1.770.25651500.22352688283895
1.77-1.810.27221280.2122692282095
1.81-1.850.25371450.21422786293199
1.85-1.90.25651550.21812763291899
1.9-1.950.22531590.22612778293799
1.95-2.010.23631270.20892810293799
2.01-2.070.2091550.19842774292999
2.07-2.150.2231440.2052763290799
2.15-2.230.21671500.19872804295499
2.23-2.340.22971590.20042757291698
2.34-2.460.22831350.19742751288697
2.46-2.610.22591290.19172639276894
2.61-2.810.22951430.18972792293598
2.81-3.10.21151400.18742754289497
3.1-3.550.19021390.17582773291298
3.55-4.470.16831380.15352837297599
4.47-39.20.16821360.16222810294696

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