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- PDB-7zr2: Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike... -

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Basic information

Entry
Database: PDB / ID: 7zr2
TitleCrystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
Components
  • Spike protein S2'
  • Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1
KeywordsANTIVIRAL PROTEIN / coiled-coil
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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 ...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 / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsCamara-Artigas, A. / Gavira, J.A. / Cano-Munoz, M. / Polo-Megias, D. / Conejero-Lara, F.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentCV-26565 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity.
Authors: Cano-Munoz, M. / Polo-Megias, D. / Camara-Artigas, A. / Gavira, J.A. / Lopez-Rodriguez, M.J. / Laumond, G. / Schmidt, S. / Demiselle, J. / Bahram, S. / Moog, C. / Conejero-Lara, F.
History
DepositionMay 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1
B: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)31,2512
Polymers31,2512
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-27 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.777, 37.374, 43.911
Angle α, β, γ (deg.)90.000, 95.670, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1


Mass: 26577.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Plasmid: pET303 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC2
#2: Protein/peptide Spike protein S2'


Mass: 4673.132 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide V39E derived from the S2 HR2 sequence.The amino terminal is acetylated and the carboxyl-terminal is amidated. The peptide was C-terminally tagged with a SGGY sequence to ...Details: Synthetic peptide V39E derived from the S2 HR2 sequence.The amino terminal is acetylated and the carboxyl-terminal is amidated. The peptide was C-terminally tagged with a SGGY sequence to confer UV absorption at 280 nm.
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.6 % / Mosaicity: 0.13 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M sodium HEPES, 20% (w/v) PEG4000, 10% (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.45→18.92 Å / Num. obs: 46236 / % possible obs: 96.3 % / Redundancy: 3 % / Biso Wilson estimate: 15.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.039 / Rrim(I) all: 0.071 / Net I/σ(I): 9.4 / Num. measured all: 138163 / Scaling rejects: 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.482.40.786460319300.6160.5750.981.275.4
7.67-18.923.10.0299503050.9990.0180.03526.386.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LXT

6lxt


Resolution: 1.45→18.8 Å / SU ML: 0.1672 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 21.6976
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.209 2265 4.9 %
Rwork0.174 43922 -
obs0.1757 46187 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.63 Å2
Refinement stepCycle: LAST / Resolution: 1.45→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 0 304 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732036
X-RAY DIFFRACTIONf_angle_d0.71692745
X-RAY DIFFRACTIONf_chiral_restr0.048332
X-RAY DIFFRACTIONf_plane_restr0.0046364
X-RAY DIFFRACTIONf_dihedral_angle_d14.7438767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.31291060.27652149X-RAY DIFFRACTION75.67
1.48-1.520.27971250.23272567X-RAY DIFFRACTION89.38
1.52-1.550.26361510.21722701X-RAY DIFFRACTION96.25
1.55-1.60.26661400.20012819X-RAY DIFFRACTION99.53
1.6-1.640.23871620.17872843X-RAY DIFFRACTION99.5
1.64-1.70.22661620.17672788X-RAY DIFFRACTION98.93
1.7-1.760.22351570.16822794X-RAY DIFFRACTION98.86
1.76-1.830.21541240.16222831X-RAY DIFFRACTION98.7
1.83-1.910.21981370.15812822X-RAY DIFFRACTION99.06
1.91-2.010.22211270.16532814X-RAY DIFFRACTION98.59
2.01-2.140.20271620.14742779X-RAY DIFFRACTION97.55
2.14-2.30.17411440.14832822X-RAY DIFFRACTION98.31
2.3-2.530.18451530.15332781X-RAY DIFFRACTION97.7
2.53-2.90.20761360.16942809X-RAY DIFFRACTION96.68
2.9-3.650.20861430.17272793X-RAY DIFFRACTION96.45
3.65-18.80.19531360.19092810X-RAY DIFFRACTION94.09

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