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- PDB-7ek6: Structure of viral peptides IPB19/N52 -

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Basic information

Entry
Database: PDB / ID: 7ek6
TitleStructure of viral peptides IPB19/N52
Components(Spike protein S2) x 2
KeywordsVIRAL PROTEIN / SARS-CoV-2 / spike protein / membrane fusion / fusion inhibitor / lipopeptide
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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.243 Å
AuthorsYu, D. / Qin, B. / Cui, S. / He, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81630061 China
CitationJournal: Emerg Microbes Infect / Year: 2021
Title: Structure-based design and characterization of novel fusion-inhibitory lipopeptides against SARS-CoV-2 and emerging variants.
Authors: Yu, D. / Zhu, Y. / Jiao, T. / Wu, T. / Xiao, X. / Qin, B. / Chong, H. / Lei, X. / Ren, L. / Cui, S. / Wang, J. / He, Y.
History
DepositionApr 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)9,9072
Polymers9,9072
Non-polymers00
Water1,802100
1
A: Spike protein S2
B: Spike protein S2

A: Spike protein S2
B: Spike protein S2

A: Spike protein S2
B: Spike protein S2


Theoretical massNumber of molelcules
Total (without water)29,7216
Polymers29,7216
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12100 Å2
ΔGint-88 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.233, 38.233, 317.329
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1339-

HOH

21A-1355-

HOH

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Components

#1: Protein Spike protein S2


Mass: 5554.122 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#2: Protein/peptide Spike protein S2


Mass: 4352.916 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.26M Sodium phosphate monobasic monohydrate, 0.14M Potassium phosphate dibasic, pH 5.6

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Data collection

DiffractionMean temperature: 296 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.24→32.932 Å / Num. obs: 25377 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 31.47 % / Biso Wilson estimate: 15.58 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.058 / Χ2: 0.95 / Net I/σ(I): 35
Reflection shellResolution: 1.24→3.71 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3470 / CC1/2: 0.81 / Χ2: 0.57 / % possible all: 84

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LXT

6lxt


Resolution: 1.243→32.932 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 1276 5.03 %Random
Rwork0.1731 24071 --
obs0.1737 25347 96.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.8 Å2 / Biso mean: 28.383 Å2 / Biso min: 9.78 Å2
Refinement stepCycle: final / Resolution: 1.243→32.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms587 0 0 100 687
Biso mean---35.75 -
Num. residues----77
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.243-1.29280.32881170.3249213080
1.2928-1.35160.29821320.2395254993
1.3516-1.42290.22481360.21022709100
1.4229-1.51210.19741440.18712697100
1.5121-1.62880.17851360.15672716100
1.6288-1.79270.19331420.15862757100
1.7927-2.05210.1681650.15982738100
2.0521-2.58520.14321310.14322828100
2.5852-3.710.19581730.17982947100

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