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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 / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion ...virion component / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / 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 / symbiont entry into host cell / 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: Cell Rep / Year: 2025
Title: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation.
Authors: Eduardo Olmedillas / Roshan R Rajamanickam / Ruben Diaz Avalos / Fernanda Ana-Sosa-Batiz / Dawid Zyla / Michelle A Zandonatti / Stephanie S Harkins / Sujan Shresta / Kathryn M Hastie / Erica Ollmann Saphire /
Abstract: The continued emergence of SARS-CoV-2 variants necessitates the development of immunogens that promote broad and durable immunity. The SARS-CoV-2 S2 fusion subunit drives viral entry and has sequence ...The continued emergence of SARS-CoV-2 variants necessitates the development of immunogens that promote broad and durable immunity. The SARS-CoV-2 S2 fusion subunit drives viral entry and has sequence conservation among coronavirus spike proteins. Therefore, S2 could represent an immunogen to boost broadly reactive antibodies. However, when expressed without the S1 domain, metastable S2 irreversibly collapses into the post-fusion six-helix bundle conformation. Beyond well-characterized RBD/NTD shifts, biophysical measurements indicate that spike exhibits reversible "breathing" motions. Using an engineered S2-only antigen that retains the pre-fusion viral surface conformation, we isolated S2-specific antibodies from convalescent and vaccinated individuals. One mAb was used to solve a high-resolution cryo-EM structure of pre-fusion S2. Our structure reveals that, relative to intact spike, engineered S2 adopts a more "open" conformation with stabilizing intermolecular interactions at the trimer base and fusion peptide repositioning. This structure could advance next-generation "booster" immunogens and illuminate potential breathing adjustments of the coronavirus spike.
History
DepositionDec 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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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