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- PDB-7wxz: Crystal structure of the recombinant protein HR121 from the S2 pr... -

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Basic information

Entry
Database: PDB / ID: 7wxz
TitleCrystal structure of the recombinant protein HR121 from the S2 protein of SARS-CoV-2
ComponentsSpike protein S2'
KeywordsVIRAL PROTEIN / SARS-CoV-2 / S2 / recombinant protein / HR121 / fusion intermediate
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 / symbiont-mediated suppression of host innate immune response / 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
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsZheng, Y.T. / Ouyang, S. / Pang, W. / Lu, Y. / Zhao, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res. / Year: 2022
Title: A variant-proof SARS-CoV-2 vaccine targeting HR1 domain in S2 subunit of spike protein.
Authors: Pang, W. / Lu, Y. / Zhao, Y.B. / Shen, F. / Fan, C.F. / Wang, Q. / He, W.Q. / He, X.Y. / Li, Z.K. / Chen, T.T. / Yang, C.X. / Li, Y.Z. / Xiao, S.X. / Zhao, Z.J. / Huang, X.S. / Luo, R.H. / ...Authors: Pang, W. / Lu, Y. / Zhao, Y.B. / Shen, F. / Fan, C.F. / Wang, Q. / He, W.Q. / He, X.Y. / Li, Z.K. / Chen, T.T. / Yang, C.X. / Li, Y.Z. / Xiao, S.X. / Zhao, Z.J. / Huang, X.S. / Luo, R.H. / Yang, L.M. / Zhang, M. / Dong, X.Q. / Li, M.H. / Feng, X.L. / Zhou, Q.C. / Qu, W. / Jiang, S. / Ouyang, S. / Zheng, Y.T.
History
DepositionFeb 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 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

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Assembly

Deposited unit
A: Spike protein S2'
B: Spike protein S2'
C: Spike protein S2'
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)88,8274
Polymers88,8274
Non-polymers00
Water905
1
A: Spike protein S2'
B: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)44,4132
Polymers44,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-101 kcal/mol
Surface area17470 Å2
MethodPISA
2
C: Spike protein S2'
D: Spike protein S2'


Theoretical massNumber of molelcules
Total (without water)44,4132
Polymers44,4132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-101 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.160, 51.730, 119.160
Angle α, β, γ (deg.)90.000, 95.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Spike protein S2'


Mass: 22206.678 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fusion protein HR121
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2
Production host: Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium fluoride, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2021
RadiationMonochromator: ROTATING ANODE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.41→32.46 Å / Num. obs: 30888 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 72.89 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.62
Reflection shellResolution: 2.41→2.496 Å / Num. unique obs: 30877 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LXT

6lxt


Resolution: 2.41→32.46 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 39.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2937 1502 4.88 %
Rwork0.249 29285 -
obs0.2511 30877 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.86 Å2 / Biso min: 56.48 Å2
Refinement stepCycle: final / Resolution: 2.41→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 0 5 5563
Biso mean---77.44 -
Num. residues----738
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.41-2.490.55211330.45932617100
2.49-2.580.38051250.3978263799
2.58-2.680.41811490.35142649100
2.68-2.80.37711670.33322591100
2.8-2.950.36781180.3074268199
2.95-3.130.39511190.30032671100
3.13-3.380.35241200.28662674100
3.38-3.710.32061500.25942666100
3.72-4.250.25981610.21862663100
4.25-5.350.25981310.2085268599

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