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- EMDB-14724: SARS CoV Spike protein, Open conformation -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-14724
TitleSARS CoV Spike protein, Open conformation
Map data
Sample
  • Complex: SARS CoV Spike protein, open conformation
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / virion component / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / virion component / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
Fibritin / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome-related coronavirus / Tequatrovirus T4
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsToelzer C / Gupta K / Yadav SKN / Buzas D / Borucu U / Schaffitzel C / Berger I
Funding support United Kingdom, 7 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P000940/1 United Kingdom
Wellcome Trust202904/Z/16/Z United Kingdom
Wellcome Trust206181/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
Wellcome Trust210701/Z/18/Z United Kingdom
Wellcome Trust106115/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R000484/1 United Kingdom
CitationJournal: Sci Adv / Year: 2022
Title: The free fatty acid-binding pocket is a conserved hallmark in pathogenic β-coronavirus spike proteins from SARS-CoV to Omicron.
Authors: Christine Toelzer / Kapil Gupta / Sathish K N Yadav / Lorna Hodgson / Maia Kavanagh Williamson / Dora Buzas / Ufuk Borucu / Kyle Powers / Richard Stenner / Kate Vasileiou / Frederic Garzoni ...Authors: Christine Toelzer / Kapil Gupta / Sathish K N Yadav / Lorna Hodgson / Maia Kavanagh Williamson / Dora Buzas / Ufuk Borucu / Kyle Powers / Richard Stenner / Kate Vasileiou / Frederic Garzoni / Daniel Fitzgerald / Christine Payré / Gunjan Gautam / Gérard Lambeau / Andrew D Davidson / Paul Verkade / Martin Frank / Imre Berger / Christiane Schaffitzel /
Abstract: As coronavirus disease 2019 (COVID-19) persists, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S ...As coronavirus disease 2019 (COVID-19) persists, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) emerge, accumulating spike (S) glycoprotein mutations. S receptor binding domain (RBD) comprises a free fatty acid (FFA)-binding pocket. FFA binding stabilizes a locked S conformation, interfering with virus infectivity. We provide evidence that the pocket is conserved in pathogenic β-coronaviruses (β-CoVs) infecting humans. SARS-CoV, MERS-CoV, SARS-CoV-2, and VOCs bind the essential FFA linoleic acid (LA), while binding is abolished by one mutation in common cold-causing HCoV-HKU1. In the SARS-CoV S structure, LA stabilizes the locked conformation, while the open, infectious conformation is devoid of LA. Electron tomography of SARS-CoV-2-infected cells reveals that LA treatment inhibits viral replication, resulting in fewer deformed virions. Our results establish FFA binding as a hallmark of pathogenic β-CoV infection and replication, setting the stage for FFA-based antiviral strategies to overcome COVID-19.
History
DepositionApr 5, 2022-
Header (metadata) releaseFeb 15, 2023-
Map releaseFeb 15, 2023-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14724.png

Downloads & links

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Map

FileDownload / File: emd_14724.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 220 pix.
= 231. Å		1.05 Å/pix.
x 220 pix.
= 231. Å		1.05 Å/pix.
x 220 pix.
= 231. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.1677782 - 0.2540892
Average (Standard dev.)0.0010241355 (±0.009044699)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 230.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14724_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14724_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14724_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 : SARS CoV Spike protein, open conformation

EntireName: SARS CoV Spike protein, open conformation
Components
  • Complex: SARS CoV Spike protein, open conformation
    • Protein or peptide: Spike glycoprotein,Fibritin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SARS CoV Spike protein, open conformation

SupramoleculeName: SARS CoV Spike protein, open conformation / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome-related coronavirus
Molecular weightTheoretical: 414 KDa

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Tequatrovirus T4
Molecular weightTheoretical: 136.201797 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SDLDRCTTFD DVQAPNYTQH TSSMRGVYYP DEIFRSDTLY LTQDLFLPFY SNVTGFHTIN HTFDNPVIPF KDGIYFAATE KSNVVRGWV FGSTMNNKSQ SVIIINNSTN VVIRACNFEL CDNPFFAVSK PMGTQTHTMI FDNAFNCTFE YISDAFSLDV S EKSGNFKH ...String:
SDLDRCTTFD DVQAPNYTQH TSSMRGVYYP DEIFRSDTLY LTQDLFLPFY SNVTGFHTIN HTFDNPVIPF KDGIYFAATE KSNVVRGWV FGSTMNNKSQ SVIIINNSTN VVIRACNFEL CDNPFFAVSK PMGTQTHTMI FDNAFNCTFE YISDAFSLDV S EKSGNFKH LREFVFKNKD GFLYVYKGYQ PIDVVRDLPS GFNTLKPIFK LPLGINITNF RAILTAFSPA QDTWGTSAAA YF VGYLKPT TFMLKYDENG TITDAVDCSQ NPLAELKCSV KSFEIDKGIY QTSNFRVVPS GDVVRFPNIT NLCPFGEVFN ATK FPSVYA WERKKISNCV ADYSVLYNST FFSTFKCYGV SATKLNDLCF SNVYADSFVV KGDDVRQIAP GQTGVIADYN YKLP DDFMG CVLAWNTRNI DATSTGNYNY KYRYLRHGKL RPFERDISNV PFSPDGKPCT PPALNCYWPL NDYGFYTTTG IGYQP YRVV VLSFELLNAP ATVCGPKLST DLIKNQCVNF NFNGLTGTGV LTPSSKRFQP FQQFGRDVSD FTDSVRDPKT SEILDI SPC SFGGVSVITP GTNASSEVAV LYQDVNCTDV STAIHADQLT PAWRIYSTGN NVFQTQAGCL IGAEHVDTSY ECDIPIG AG ICASYHTVSL LRSTSQKSIV AYTMSLGADS SIAYSNNTIA IPTNFSISIT TEVMPVSMAK TSVDCNMYIC GDSTECAN L LLQYGSFCTQ LNRALSGIAA EQDRNTREVF AQVKQMYKTP TLKYFGGFNF SQILPDPLKP TKRSFIEDLL FNKVTLADA GFMKQYGECL GDINARDLIC AQKFNGLTVL PPLLTDDMIA AYTAALVSGT ATAGWTFGAG AALQIPFAMQ MAYRFNGIGV TQNVLYENQ KQIANQFNKA ISQIQESLTT TSTALGKLQD VVNQNAQALN TLVKQLSSNF GAISSVLNDI LSRLDKVEAE V QIDRLITG RLQSLQTYVT QQLIRAAEIR ASANLAATKM SECVLGQSKR VDFCGKGYHL MSFPQAAPHG VVFLHVTYVP SQ ERNFTTA PAICHEGKAY FPREGVFVFN GTSWFITQRN FFSPQIITTD NTFVSGNCDV VIGIINNTVY DPLQPELDSF KEE LDKYFK NHTSPDVDLG DISGINASVV NIQKEIDRLN EVAKNLNESL IDLQELGKYE QYIKPSGRLV PRGSPGSGYI PEAP RDGQA YVRKDGEWVL LSTFLGHHHH HH

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 23 / 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

Concentration0.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 6600 / Average exposure time: 12.0 sec. / Average electron dose: 62.65 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1724689
Startup modelType of model: EMDB MAP
EMDB ID:

11146

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 81242
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6acd

Output model

PDB-7zh5:
SARS CoV Spike protein, Open conformation

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