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- EMDB-42985: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open ... -

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Entry
Database: EMDB / ID: EMD-42985
TitleStructure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Map data
Sample
  • Complex: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation in complex with the 6C10 Fab
    • Complex: Fab fragment of the 6C10 human monoclonal antibody
      • Protein or peptide: Variable domain of the light chain from the human antibody 6C10
      • Protein or peptide: Variable domain of the heavy chain from the human antibody 6C10
    • Complex: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
      • Protein or peptide: Spike protein S2,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSARS-CoV-2 / Spike / S2 / VIRAL PROTEIN
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 / Homo sapiens (human) / Mus musculus molossinus (Japanese wild mouse) / Tequatrovirus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsOlmedillas E / Diaz R / Hastie K / Ollmann-Saphire E
Funding support United States, 1 items
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, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42985.png

Downloads & links

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Map

FileDownload / File: emd_42985.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 280 pix.
= 369.6 Å		1.32 Å/pix.
x 280 pix.
= 369.6 Å		1.32 Å/pix.
x 280 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.40506163 - 1.5480001
Average (Standard dev.)-0.0010804561 (±0.039018154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42985_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42985_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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

EntireName: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation in complex with the 6C10 Fab
Components
  • Complex: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation in complex with the 6C10 Fab
    • Complex: Fab fragment of the 6C10 human monoclonal antibody
      • Protein or peptide: Variable domain of the light chain from the human antibody 6C10
      • Protein or peptide: Variable domain of the heavy chain from the human antibody 6C10
    • Complex: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
      • Protein or peptide: Spike protein S2,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open ...

SupramoleculeName: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation in complex with the 6C10 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Wuhan
Molecular weightTheoretical: 280 KDa

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Supramolecule #2: Fab fragment of the 6C10 human monoclonal antibody

SupramoleculeName: Fab fragment of the 6C10 human monoclonal antibody / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human) / Organ: Immune system

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Supramolecule #3: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open ...

SupramoleculeName: Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus molossinus (Japanese wild mouse)

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Macromolecule #1: Spike protein S2,Fibritin

MacromoleculeName: Spike protein S2,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 64.292461 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: SIIAYTMSLG AENSVACSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQ EVFAQVKQCY KTPPIKDFGG FNFSQILPDP SKPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL I CAQKFNGL ...String:
SIIAYTMSLG AENSVACSNN SIAIPTNFTI SVTTEILPVS MTKTSVDCTM YICGDSTECS NLLLQYGSFC TQLNRALTGI AVEQDKNTQ EVFAQVKQCY KTPPIKDFGG FNFSQILPDP SKPSKRSPIE DLLFNKVTLA DAGFIKQYGD CLGDIAARDL I CAQKFNGL TVLPPLLTDE MIAQYTSCLL AGTICSGWTF GAGPALQIPF PMQMAYRFNG IGVTQNVLYE NQKLIANQFN SA IGKIQDS LSSTPSALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDILSRLDKP EAEVQIDRLI TGRLQSLQTY VTQ QLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQSA PHGVVFLHVT YVPAQEKNFT TAPAICHDGK AHFP REGVF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQPEL DSFKEELDKY FKNHTSPDVD LGDIS GINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQYIKGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLLEVL FQGPAG WSH PQFEKGGGSG GGSGGGSWSH PQFEK

UniProtKB: Spike glycoprotein, Fibritin

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Macromolecule #2: Variable domain of the light chain from the human antibody 6C10

MacromoleculeName: Variable domain of the light chain from the human antibody 6C10
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.696993 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
AIRMTQSPST LSVSPGERAT LSCRASQSVS SYLAWYQHKP GQAPRLLVYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDFAVYYCQ QYNNWPPPFT FGPGTKVDI

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Macromolecule #3: Variable domain of the heavy chain from the human antibody 6C10

MacromoleculeName: Variable domain of the heavy chain from the human antibody 6C10
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.913493 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVQSGAE VRKPGASVKV SCKASGYTFT GYYIHWVRQA PGQGLEWMGW INPNSGGTNY AQKFQGWVIM TRDTSISTAY MELSRLTSD DTAVYYCARC GARSYYYDSG DYCAFDIWGQ GTVVTV

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
200.0 mMNaCl

Details: Filtered and degased
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.001 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 6 seconds blotting time at force 0.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.1 K / Max: 90.2 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 2 / Number real images: 12444 / Average exposure time: 1.4 sec. / Average electron dose: 50.0 e/Å2 / Details: Two datasets
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 1.973 µm / Calibrated defocus min: 0.481 µm / Calibrated magnification: 75757 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 407314
Startup modelType of model: INSILICO MODEL
In silico model: The images were transferred to cryoSparc and ab initio model built
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 408064
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 200000 / Software - Name: cryoSPARC (ver. 4.0)

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Atomic model buiding 1

Initial modelPDB ID:

6xkl


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 150 / Target criteria: Cross-correlation coefficient
Output model

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

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Atomic model buiding 2

Initial modelPDB ID:

6xkl


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsCOOT model building and refinament
RefinementProtocol: OTHER
Output model

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

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