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- EMDB-34418: Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfid... -

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Basic information

Entry
Database: EMDB / ID: EMD-34418
TitleStructure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-112 Conformation
Map data
Sample
  • Complex: SARS-CoV-1 spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: LINOLEIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA
KeywordsPROTEIN ENGINEERING / SPIKE PROTEIN / SARS-COV-1 / SARS-COV / VIRAL PROTEIN
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / 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 ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / 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 / 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 ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV / 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
Biological speciesSevere acute respiratory syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsZhang X / Li Z / Liu Y / Wang J / Fu L / Wang P / He J / Xiong X
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Life Sci Alliance / Year: 2023
Title: Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes.
Authors: Xixi Zhang / Zimu Li / Yanjun Zhang / Yutong Liu / Jingjing Wang / Banghui Liu / Qiuluan Chen / Qian Wang / Lutang Fu / Peiyi Wang / Xiaolin Zhong / Liang Jin / Qihong Yan / Ling Chen / Jun ...Authors: Xixi Zhang / Zimu Li / Yanjun Zhang / Yutong Liu / Jingjing Wang / Banghui Liu / Qiuluan Chen / Qian Wang / Lutang Fu / Peiyi Wang / Xiaolin Zhong / Liang Jin / Qihong Yan / Ling Chen / Jun He / Jincun Zhao / Xiaoli Xiong /
Abstract: SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers ...SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers adopting locked conformations are tightly packed featuring structural elements incompatible with RBD in the "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably because of their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures with other available spike structures of SARS-related CoVs to identify conserved features and discuss their possible functions.
History
DepositionSep 30, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_34418.png

Downloads & links

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Map

FileDownload / File: emd_34418.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 336 pix.
= 367.92 Å		1.1 Å/pix.
x 336 pix.
= 367.92 Å		1.1 Å/pix.
x 336 pix.
= 367.92 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.17281643 - 0.328425
Average (Standard dev.)0.00018212417 (±0.006452894)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 367.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34418_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34418_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_34418_half_map_2.map
Projections & Slices
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Sample components

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Entire : SARS-CoV-1 spike protein

EntireName: SARS-CoV-1 spike protein
Components
  • Complex: SARS-CoV-1 spike protein
    • Protein or peptide: Spike glycoprotein
  • Ligand: LINOLEIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: BILIVERDINE IX ALPHA

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Supramolecule #1: SARS-CoV-1 spike protein

SupramoleculeName: SARS-CoV-1 spike protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus / Strain: SARS coronavirus Tor2
Molecular weightTheoretical: 410 KDa

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus
Molecular weightTheoretical: 136.679359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGTDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYFA ATEKSNVVR GWVFGSTMNN KSQSVIIINN STNVVIRACN FELCDNPFFA VSKPMGTQTH TMIFDNAFNC TFEYISDAFS L DVSEKSGN ...String:
ETGTDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYFA ATEKSNVVR GWVFGSTMNN KSQSVIIINN STNVVIRACN FELCDNPFFA VSKPMGTQTH TMIFDNAFNC TFEYISDAFS L DVSEKSGN FKHLREFVFK NKDGFLYVYK GYQPIDVVRD LPSGFNTLKP IFKLPLGINI TNFRAILTAF SPAQDIWGTS AA AYFVGYL KPTTFMLKYD ENGTITDAVD CSQNPLAELK CSVKSFEIDK GIYQTSNFRV VPSGDVVRFP NITNLCPFGE VFN ATKFPS VYAWERKKIS NCVADYSVLY NSTFFSTFKC YGVCATKLND LCFSNVYADS FVVKGDDVRQ IAPGQTGVIA DYNY KLPDD FMGCVLAWNT RNIDATSTGN YNYKYRYLRH GKLRPFERDI SNVPFSPDGK PCTPPALNCY WPLNDYGFYT TTGIG YQPY RVVVLSFELL NAPATVCGPK LSTDLIKNQC VNFNFNGLTG TGVLTPSSKR FQPFQQFGRD VSDFTDSVRD PKTSEI LDI SPCSFGGVSV ITPGTNASSE VAVLYQDVNC TDVSTAIHAD QLTPAWRIYS TGNNVFQTQA GCLIGAEHVD TSYECDI PI GAGICASYHT VSLLRSTSQK SIVAYTMSLG ADSSIAYSNN TIAIPTNFSI SITTEVMPVS MAKTSVDCNM YICGDSTE C ANLLLQYGSF CTQLNRALSG IAAEQDRNTR EVFAQVKQMY KTPTLKYFGG FNFSQILPDP LKPTKRSFIE DLLFNKVTL ADAGFMKQYG ECLGDINARD LICAQKFNGL TVLPPLLTDD MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLY ENQKQIANQF NKAISQIQES LTTTSTALGK LQDVVNQNAQ ALNTLVKQLS SNFGAISSVL NDILSRLCKV E AEVQIDRL ITGRLQSLQT YVTQQLIRAA EIRASANLAA TKMSECVLGQ SKRVDFCGKG YHLMSFPQAA PHGVVFLHVT YV PSQERNF TTAPAICHEG KAYFPREGVF VFNGTSWFIT QRNFFSPQII TTDNTFVSGN CDVVIGIINN TVYDPLQPEL DSF KEELDK YFKNHTSPDV DLGDISGINA SVVNIQKEID RLNEVAKNLN ESLIDLQELG KYEQYIKGSG RENLYFQGGG GSGY IPEAP RDGQAYVRKD GEWVLLSTFL GHHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #2: LINOLEIC ACID

MacromoleculeName: LINOLEIC ACID / type: ligand / ID: 2 / Number of copies: 3 / Formula: EIC
Molecular weightTheoretical: 280.445 Da
Chemical component information

ChemComp-EIC:
LINOLEIC ACID

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 46 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: BILIVERDINE IX ALPHA

MacromoleculeName: BILIVERDINE IX ALPHA / type: ligand / ID: 4 / Number of copies: 3 / Formula: BLA
Molecular weightTheoretical: 582.646 Da
Chemical component information

ChemComp-BLA:
BILIVERDINE IX ALPHA

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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

Concentration4.7 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
1.0588236 mMKH2PO4Potassium Phosphate monobasic
155.17241 mMNaClSodium Chloride
2.966418 mMNa2HPO4Sodium Phosphate dibasic

Details: Gibco PBS C10010
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.37 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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: 81000
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: 4604239 / Details: Particles were picked by Warp v1.09
Startup modelType of model: EMDB MAP
EMDB ID:

11329

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 91477
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

7xtz

,

7xu2

)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 65
Output model

PDB-8h0y:
Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-112 Conformation

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