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- PDB-8v5v: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open ... -

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Basic information

Entry
Database: PDB / ID: 8v5v
TitleStructure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Components
  • Spike protein S2,Fibritin
  • Variable domain of the heavy chain from the human antibody 6C10
  • Variable domain of the light chain from the human antibody 6C10
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Spike / S2
Function / homology
Function and homology information


virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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
Fibritin C-terminal / Fibritin C-terminal region / 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. ...Fibritin C-terminal / Fibritin C-terminal region / 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
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Tequatrovirus T4
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsOlmedillas, E. / Diaz, R. / Hastie, K. / Ollmann-Saphire, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI165072 United States
CitationJournal: To Be Published
Title: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Authors: Olmedillas, E. / Diaz, R. / Hastie, K. / Ollmann-Saphire, E.
History
DepositionDec 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Spike protein S2,Fibritin
E: Spike protein S2,Fibritin
F: Spike protein S2,Fibritin
d: Variable domain of the light chain from the human antibody 6C10
g: Variable domain of the light chain from the human antibody 6C10
f: Variable domain of the heavy chain from the human antibody 6C10
c: Variable domain of the heavy chain from the human antibody 6C10
e: Variable domain of the light chain from the human antibody 6C10
b: Variable domain of the heavy chain from the human antibody 6C10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,30027
Polymers269,7099
Non-polymers4,59118
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Spike protein S2,Fibritin / Collar protein / Whisker antigen control protein


Mass: 64292.461 Da / Num. of mol.: 3
Mutation: F817P,A892P,A899P,A942P,V987P,Y707C,T883C,Y788C,A876C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) Tequatrovirus T4
Gene: S, 2, wac / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2, UniProt: P10104
#2: Antibody Variable domain of the light chain from the human antibody 6C10


Mass: 11696.993 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Variable domain of the heavy chain from the human antibody 6C10


Mass: 13913.493 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation in complex with the 6C10 FabCOMPLEX#1-#30RECOMBINANT
2Fab fragment of the 6C10 human monoclonal antibodyCOMPLEX#2-#31RECOMBINANT
3Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformationCOMPLEX#11RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.47 MDaYES
210.15 MDaYES
310.28 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrainOrgan
21Severe acute respiratory syndrome coronavirus 22697049Wuhan
32Homo sapiens (human)9606Immune system
43Mus musculus molossinus (Japanese wild mouse)57486
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Mus musculus molossinus (Japanese wild mouse)57486Chinesse hammster ovariumphCMV
32Mus musculus molossinus (Japanese wild mouse)57486Chinesse hammster ovariumphCMV
43Mus musculus molossinus (Japanese wild mouse)57486Chinesse hammster ovariumphCMV
Buffer solutionpH: 8 / Details: Filtered and degased
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisC4H11NO31
2200 mMNaCl1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 6 seconds blotting time at force 0

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 75757 X / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 481 nm / Calibrated defocus max: 1973 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 90.2 K / Temperature (min): 80.1 K / Residual tilt: 0.1 mradians
Image recordingAverage exposure time: 1.4 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 12444 / Details: Two datasets
Image scansSampling size: 5 µm / Width: 6000 / Height: 4000

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Processing

EM software
IDNameVersionCategoryFitting-ID
1Warp1.09particle selection
2EPU2.12image acquisition
4Warp1.09CTF correction
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
11cryoSPARC4classification
12cryoSPARC43D reconstruction
13PHENIX1.20.1_4487:1.21model refinement1
22Coot0.9.5model refinement2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 407314
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 408064 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
IDB valueProtocolSpaceTarget criteriaDetails
1150OTHERREALCross-correlation coefficient
2OTHERCOOT model building and refinament
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16xkl

6xkl

16xkl1PDBexperimental model
26xkl

6xkl

26xkl1PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00116251
ELECTRON MICROSCOPYf_angle_d0.38122110
ELECTRON MICROSCOPYf_dihedral_angle_d3.0552301
ELECTRON MICROSCOPYf_chiral_restr0.0382523
ELECTRON MICROSCOPYf_plane_restr0.0032838

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