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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


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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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: Not published
Title: Broad Neutralizing Antibodies Against Coronaviruses.
Authors: Feng, Z. / Wilson, I.A.
History
DepositionJul 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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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