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- PDB-8aaa: Crystal structure of SARS-CoV-2 S RBD in complex with a stapled p... -

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Basic information

Entry
Database: PDB / ID: 8aaa
TitleCrystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
Components
  • Spike protein S1
  • Stapled peptide
KeywordsVIRAL PROTEIN / sRBD / Stapled peptide
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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / 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 / 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 / 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
Chem-29N / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBrear, P. / Chen, L. / Gaynor, K. / Harman, M. / Dods, R. / Hyvonen, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2023
Title: Multivalent bicyclic peptides are an effective antiviral modality that can potently inhibit SARS-CoV-2.
Authors: Gaynor, K.U. / Vaysburd, M. / Harman, M.A.J. / Albecka, A. / Jeffrey, P. / Beswick, P. / Papa, G. / Chen, L. / Mallery, D. / McGuinness, B. / Van Rietschoten, K. / Stanway, S. / Brear, P. / ...Authors: Gaynor, K.U. / Vaysburd, M. / Harman, M.A.J. / Albecka, A. / Jeffrey, P. / Beswick, P. / Papa, G. / Chen, L. / Mallery, D. / McGuinness, B. / Van Rietschoten, K. / Stanway, S. / Brear, P. / Lulla, A. / Ciazynska, K. / Chang, V.T. / Sharp, J. / Neary, M. / Box, H. / Herriott, J. / Kijak, E. / Tatham, L. / Bentley, E.G. / Sharma, P. / Kirby, A. / Han, X. / Stewart, J.P. / Owen, A. / Briggs, J.A.G. / Hyvonen, M. / Skynner, M.J. / James, L.C.
History
DepositionJun 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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 S1
B: Stapled peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0923
Polymers23,8372
Non-polymers2551
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-6 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.2, 112.2, 35.534
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-642-

HOH

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Components

#1: Protein Spike protein S1


Mass: 22074.678 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC2
#2: Protein/peptide Stapled peptide /


Mass: 1762.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-29N / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one / 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)triprop-2-en-1-one, bound form


Mass: 255.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 22% PEGSM, 2% Glycerol, 0.01M CoCl2, 0.2M MgCl2, 0.1M Bis TRIS
PH range: 8 / Temp details: l

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.848→97.168 Å / Num. obs: 13749 / % possible obs: 91.5 % / Redundancy: 19.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.058 / Rrim(I) all: 0.254 / Net I/σ(I): 9.3 / Num. measured all: 266723
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
1.848-2.06815.51.693106446860.8630.4421.7511.965.2
6.039-97.168180.093123516850.9980.0220.09623.7100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CJF

7cjf


Resolution: 1.9→48.58 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.183 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 924 -RANDOM
Rwork0.2267 ---
obs0.2272 18189 88.9 %-
Displacement parametersBiso mean: 51.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.6688 Å20 Å20 Å2
2--0.6688 Å20 Å2
3----1.3377 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 104 1771
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081733HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.932358HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d568SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes297HARMONIC5
X-RAY DIFFRACTIONt_it1733HARMONIC10
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion213SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1576SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion16.76
LS refinement shellResolution: 1.9→1.94 Å
RfactorNum. reflection% reflection
Rfree0.9356 4 -
Rwork0.8111 --
obs0.8137 396 29.54 %

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