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- PDB-7sjs: Crystal structure of SARS-CoV-2 spike stem helix peptide in compl... -

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Basic information

Entry
Database: PDB / ID: 7sjs
TitleCrystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CC40.8
Components
  • CC40.8 Fab heavy chain
  • CC40.8 Fab light chain
  • stem helix peptide of Spike protein S2'
KeywordsIMMUNE SYSTEM / SARS-CoV-2 / Antibody / Spike / S2 / stem helix
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 / 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
ACETATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.612 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI44462 United States
Bill & Melinda Gates FoundationOPP 1170236 United States
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Sci Transl Med / Year: 2022
Title: A human antibody reveals a conserved site on beta-coronavirus spike proteins and confers protection against SARS-CoV-2 infection.
Authors: Zhou, P. / Yuan, M. / Song, G. / Beutler, N. / Shaabani, N. / Huang, D. / He, W.T. / Zhu, X. / Callaghan, S. / Yong, P. / Anzanello, F. / Peng, L. / Ricketts, J. / Parren, M. / Garcia, E. / ...Authors: Zhou, P. / Yuan, M. / Song, G. / Beutler, N. / Shaabani, N. / Huang, D. / He, W.T. / Zhu, X. / Callaghan, S. / Yong, P. / Anzanello, F. / Peng, L. / Ricketts, J. / Parren, M. / Garcia, E. / Rawlings, S.A. / Smith, D.M. / Nemazee, D. / Teijaro, J.R. / Rogers, T.F. / Wilson, I.A. / Burton, D.R. / Andrabi, R.
History
DepositionOct 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 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: CC40.8 Fab heavy chain
L: CC40.8 Fab light chain
C: stem helix peptide of Spike protein S2'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,17810
Polymers48,5463
Non-polymers6317
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-32 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.925, 63.710, 121.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11H-576-

HOH

21H-583-

HOH

31L-617-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide stem helix peptide of Spike protein S2'


Mass: 2981.267 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 CC40.8 Fab heavy chain


Mass: 22741.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody CC40.8 Fab light chain


Mass: 22823.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 466 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.26
Details: 0.1 M sodium acetate buffer at pH 4.26, 0.2 M ammonium sulfate, and 28% (w/v) polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.612→50 Å / Num. obs: 54222 / % possible obs: 97 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.028 / Rrim(I) all: 0.084 / Χ2: 1.058 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.655.31.11627380.5630.4771.220.489.6
1.65-1.686.30.99528790.6780.3951.0750.40193.9
1.68-1.727.10.87629470.7530.3320.940.42596.2
1.72-1.767.60.76629180.80.2830.8190.43596.1
1.76-1.817.80.64429200.8790.2350.6880.45795.2
1.81-1.857.80.53329040.9150.1950.5690.49494.6
1.85-1.917.50.40929250.9410.1530.4380.58794.9
1.91-1.976.80.31429160.9530.1230.3380.70394.2
1.97-2.048.30.25629520.9790.0910.2730.73496.7
2.04-2.128.50.20230360.9860.0710.2150.82897.9
2.12-2.228.50.16230830.9890.0580.1720.88899.5
2.22-2.348.60.13930530.9920.050.1480.95999.8
2.34-2.488.70.11531030.9940.0410.1230.96899.4
2.48-2.678.40.09530920.9950.0350.1011.11399.5
2.67-2.948.30.07330980.9970.0260.0781.39898.9
2.94-3.3710.30.05831640.9990.0190.0611.737100
3.37-4.249.90.04831920.9990.0160.052.277100
4.24-508.40.04333020.9990.0150.0462.54498.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W41

6w41


Resolution: 1.612→30.821 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 1997 3.69 %
Rwork0.1739 52133 -
obs0.1751 54130 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.44 Å2 / Biso mean: 27.8109 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 1.612→30.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 35 459 3797
Biso mean--55.79 39.27 -
Num. residues----441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6122-1.65250.37271250.3464327686
1.6525-1.69720.27091370.2729358595
1.6972-1.74710.29071400.2164364296
1.7471-1.80350.2391380.1918360695
1.8035-1.8680.24061370.1908361094
1.868-1.94270.23291380.1902358894
1.9427-2.03110.20551430.1841370597
2.0311-2.13820.22931430.1694375998
2.1382-2.27210.24121480.17153835100
2.2721-2.44750.23141460.17823815100
2.4475-2.69370.21241470.17913843100
2.6937-3.08310.19351480.1665386499
3.0831-3.88320.1951510.15553922100
3.8832-30.8210.16831560.1618408399

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