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- PDB-8tmy: Crystal structure of SARS-CoV-2 spike stem helix peptide in compl... -

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Basic information

Entry
Database: PDB / ID: 8tmy
TitleCrystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CHM-16
Components
  • Neutralizing antibody CHM-16 Heavy Chain
  • Neutralizing antibody CHM-16 Light Chain
  • Stem helix peptide of Spike protein S2'
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / SARS-CoV-2 / Coronavirus / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion ...symbiont-mediated disruption of host tissue / Maturation of spike protein / host cell surface / Translation of Structural Proteins / Virion Assembly and Release / Lectin pathway of complement activation / host extracellular region / symbiont-mediated-mediated suppression of host tetherin activity / structural constituent of virion / Induction of Cell-Cell Fusion / positive regulation of viral entry into host cell / Initial triggering of complement / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / entry receptor-mediated virion attachment to 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 / membrane / identical protein binding / 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
Similarity search - Domain/homology
CITRATE ANION / Spike glycoprotein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsFeng, Z. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Cell Rep / Year: 2026
Title: Heterologous betacoronavirus spike immunization in non-human primates elicits antibodies that neutralize both sarbeco- and merbecoviruses.
Authors: Katharina Dueker / Tazio Capozzola / Ziqi Feng / Ryan N Lin / Jonathan Hurtado / Sandhya Bangaru / Meng Yuan / Nathan Beutler / Elijah Garcia / Wan-Ting He / Sean Callaghan / Gabriel ...Authors: Katharina Dueker / Tazio Capozzola / Ziqi Feng / Ryan N Lin / Jonathan Hurtado / Sandhya Bangaru / Meng Yuan / Nathan Beutler / Elijah Garcia / Wan-Ting He / Sean Callaghan / Gabriel Avillion / Lina Vo / Xuduo Li / Jonathan L Torres / Rami Musharrafieh / Ge Song / Nitesh Mishra / Pragati Sharma / Peter Yong / Fabio Anzanello / Katarzyna Kaczmarek Michaels / Elana Ben-Akiva / Murillo Silva / Mariane Melo / Muzamil Makhdoomi / Ethan Westfall-Gomez / William Rinaldi / Melissa Ferguson / Yana Safonova / Shane Crotty / Darrell J Irvine / Thomas Rogers / Andrew B Ward / Bryan Briney / Ian A Wilson / Dennis R Burton / Raiees Andrabi /
Abstract: In anticipation of future coronavirus (CoV) pandemics, developing vaccines that elicit broadly neutralizing antibodies (bnAbs) against diverse CoVs is critical. Here, we vaccinated rhesus macaques ...In anticipation of future coronavirus (CoV) pandemics, developing vaccines that elicit broadly neutralizing antibodies (bnAbs) against diverse CoVs is critical. Here, we vaccinated rhesus macaques with the SARS-CoV-2 spike (S)-protein, then boosted with heterologous β-CoV S-proteins to focus responses to common conserved S2 bnAb epitopes. Initial SARS-CoV-2 priming elicited receptor-binding domain (RBD)-focused responses, while MERS-CoV boosting redirected responses toward the S2 region, including the stem-helix bnAb site. Although S2-directed serum cross-neutralization was undetectable and most isolated cross-reactive monoclonal antibodies (mAbs) targeted non-neutralizing epitopes, two S2 stem-helix mAbs were identified from memory B cells. These bnAbs neutralized diverse sarbeco- and merbecoviruses, including MERS-CoV, and conferred robust in vivo protection against SARS-CoV-2 challenge. Structural studies reveal that these macaque bnAbs closely mimic human S2 stem bnAbs induced by infection. These findings provide proof-of-principle for vaccination strategies that elicit broadly protective β-coronavirus responses and highlight non-human primates as a translational model for evaluating S2-targeted immunogens.
History
DepositionJul 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Aug 26, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Stem helix peptide of Spike protein S2'
N: Stem helix peptide of Spike protein S2'
S: Stem helix peptide of Spike protein S2'
H: Neutralizing antibody CHM-16 Heavy Chain
L: Neutralizing antibody CHM-16 Light Chain
A: Neutralizing antibody CHM-16 Heavy Chain
B: Neutralizing antibody CHM-16 Light Chain
C: Neutralizing antibody CHM-16 Heavy Chain
D: Neutralizing antibody CHM-16 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,80710
Polymers149,6189
Non-polymers1891
Water00
1
M: Stem helix peptide of Spike protein S2'
A: Neutralizing antibody CHM-16 Heavy Chain
B: Neutralizing antibody CHM-16 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0624
Polymers49,8733
Non-polymers1891
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-36 kcal/mol
Surface area20060 Å2
MethodPISA
2
N: Stem helix peptide of Spike protein S2'
C: Neutralizing antibody CHM-16 Heavy Chain
D: Neutralizing antibody CHM-16 Light Chain


Theoretical massNumber of molelcules
Total (without water)49,8733
Polymers49,8733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-35 kcal/mol
Surface area20330 Å2
MethodPISA
3
S: Stem helix peptide of Spike protein S2'
H: Neutralizing antibody CHM-16 Heavy Chain
L: Neutralizing antibody CHM-16 Light Chain


Theoretical massNumber of molelcules
Total (without water)49,8733
Polymers49,8733
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-35 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.456, 73.677, 330.624
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein/peptide Stem helix peptide of Spike protein S2'


Mass: 2981.267 Da / Num. of mol.: 3 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#2: Antibody Neutralizing antibody CHM-16 Heavy Chain


Mass: 23568.428 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Antibody Neutralizing antibody CHM-16 Light Chain


Mass: 23322.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
Has ligand of interestN
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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate pH 6.5, and 1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.07→50 Å / Num. obs: 32403 / % possible obs: 94.8 % / Redundancy: 8.9 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.065 / Rrim(I) all: 0.202 / Χ2: 0.486 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.09-3.143.20.59310360.6440.8850.3140.6780.26562.9
3.14-3.23.60.54911970.6990.9070.2750.6190.27671
3.2-3.264.10.50913760.8160.9480.2490.5710.27781.8
3.26-3.334.90.50715030.8320.9530.2290.560.29189.8
3.33-3.45.80.47715670.8580.9610.2020.520.30393.7
3.4-3.486.60.45216500.8970.9720.1820.4890.31497.6
3.48-3.577.10.43116560.9180.9780.1690.4650.31199
3.57-3.667.50.39916760.9170.9780.1530.4290.32899.5
3.66-3.7780.35716640.9560.9890.1320.3820.33599.6
3.77-3.899.40.30916990.9710.9930.1050.3270.38199.6
3.89-4.039.70.27916980.9750.9940.0930.2950.416100
4.03-4.1910.10.23916870.9810.9950.0780.2520.46299.8
4.19-4.3810.50.19817010.9840.9960.0630.2080.549100
4.38-4.61110.17716980.9890.9970.0550.1850.58299.7
4.61-4.911.20.16617220.9910.9980.0510.1740.577100
4.9-5.2811.50.16117190.9920.9980.0490.1690.529100
5.28-5.8111.10.16217260.9920.9980.050.170.471100
5.81-6.6512.10.15717530.9940.9980.0470.1640.413100
6.65-8.3812.10.11317660.9970.9990.0330.1180.505100
8.38-5012.80.0719090.99910.020.0730.955100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→33.06 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2863 2017 6.26 %
Rwork0.2432 --
obs0.246 32226 93.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.07→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10106 0 13 0 10119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210354
X-RAY DIFFRACTIONf_angle_d0.58414064
X-RAY DIFFRACTIONf_dihedral_angle_d4.7491420
X-RAY DIFFRACTIONf_chiral_restr0.0421568
X-RAY DIFFRACTIONf_plane_restr0.0041809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.140.3705720.32291125X-RAY DIFFRACTION50
3.14-3.230.35921170.32491682X-RAY DIFFRACTION73
3.23-3.320.34421310.32221984X-RAY DIFFRACTION87
3.32-3.430.35751430.30282146X-RAY DIFFRACTION95
3.43-3.550.32231500.29642258X-RAY DIFFRACTION98
3.55-3.690.33511530.27832302X-RAY DIFFRACTION99
3.69-3.860.33381520.27822285X-RAY DIFFRACTION99
3.86-4.070.29881580.25042278X-RAY DIFFRACTION100
4.07-4.320.24551510.2222332X-RAY DIFFRACTION100
4.32-4.650.27161540.21272291X-RAY DIFFRACTION100
4.65-5.120.2181570.20542316X-RAY DIFFRACTION100
5.12-5.860.27741560.21822354X-RAY DIFFRACTION100
5.86-7.370.27981630.23722414X-RAY DIFFRACTION100
7.37-33.060.25071600.19832442X-RAY DIFFRACTION98

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