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- PDB-7lc8: SARS-CoV-2 spike Protein TM domain -

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Basic information

Entry
Database: PDB / ID: 7lc8
TitleSARS-CoV-2 spike Protein TM domain
ComponentsSpike protein S2'
KeywordsVIRAL PROTEIN / Coronavirus / SARS / COVID 19 / Severe acute respiratory syndrome coronavirus 2
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
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodSOLUTION NMR / simulated annealing
AuthorsFu, Q. / Chou, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI127193 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: A Trimeric Hydrophobic Zipper Mediates the Intramembrane Assembly of SARS-CoV-2 Spike.
Authors: Fu, Q. / Chou, J.J.
History
DepositionJan 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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'


Theoretical massNumber of molelcules
Total (without water)6,6023
Polymers6,6023
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1820 Å2
ΔGint-28 kcal/mol
Surface area4440 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Spike protein S2'


Mass: 2200.703 Da / Num. of mol.: 3 / Fragment: TM domain, residues 1217-1237 / Mutation: M1229L, M1233L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
116isotropic12D 1H-15N HSQC
126isotropic23D HNCA
136isotropic23D HNCO
143isotropic23D 1H-15N NOESY
154isotropic23D HNCO
165isotropic12D 1H-15N HSQC NH2 only

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
bicelle355 mM [U-99% 2H] 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM [U-99% 2H] 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-13C; U-15N] Spike glycoprotein, 90% H2O/10% D2O15N 13C90% H2O/10% D2O
bicelle455 mM [U-99% 2H] 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM [U-99% 2H] 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-13C; U-15N; U-2H] Spike glycoprotein, 90% H2O/10% D2Omixed(15N, 2H | 13C)90% H2O/10% D2O
bicelle555 mM 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-15N; U-2H] Spike glycoprotein, 90% H2O/10% D2O15N 2H90% H2O/10% D2O
bicelle655 mM 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-13C; U-15N; U-2H] Spike glycoprotein, 90% H2O/10% D2O15N 13C 2H90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
55 mM1,2-dimyristoyl-sn-Glycero-3-Phosphocholine[U-99% 2H]3
100 mM1,2-dihexanoyl-sn-Glycero-3-Phosphocholine[U-99% 2H]3
20 mMTRISnatural abundance3
0.02 %sodium azidenatural abundance3
20 mMsodium chloridenatural abundance3
1 mMSpike glycoprotein[U-13C; U-15N]3
55 mM1,2-dimyristoyl-sn-Glycero-3-Phosphocholine[U-99% 2H]4
100 mM1,2-dihexanoyl-sn-Glycero-3-Phosphocholine[U-99% 2H]4
20 mMTRISnatural abundance4
0.02 %sodium azidenatural abundance4
20 mMsodium chloridenatural abundance4
1 mMSpike glycoprotein[U-13C; U-15N; U-2H]4
55 mM1,2-dimyristoyl-sn-Glycero-3-Phosphocholinenatural abundance5
100 mM1,2-dihexanoyl-sn-Glycero-3-Phosphocholinenatural abundance5
20 mMTRISnatural abundance5
0.02 %sodium azidenatural abundance5
20 mMsodium chloridenatural abundance5
1 mMSpike glycoprotein[U-15N; U-2H]5
55 mM1,2-dimyristoyl-sn-Glycero-3-Phosphocholinenatural abundance6
100 mM1,2-dihexanoyl-sn-Glycero-3-Phosphocholinenatural abundance6
20 mMTRISnatural abundance6
0.02 %sodium azidenatural abundance6
20 mMsodium chloridenatural abundance6
1 mMSpike glycoprotein[U-13C; U-15N; U-2H]6
Sample conditionsIonic strength: 20 mM / Label: q-0.55 / pH: 6.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.48Schwieters, Kuszewski, Tjandra and Clorestructure calculation
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 14

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