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- EMDB-30071: Cryo-EM structure of SADS-CoV spike -

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Basic information

Entry
Database: EMDB / ID: EMD-30071
TitleCryo-EM structure of SADS-CoV spike
Map data
Sample
  • Complex: SADS-CoV spike trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSADS-CoV spike / VIRAL PROTEIN
Function / homology
Function and homology information


host cell membrane / endocytosis involved in viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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
Biological speciesSwine acute diarrhea syndrome coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsOuyang S / Hongxin G
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Virol / Year: 2020
Title: Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins.
Authors: Hongxin Guan / Youwang Wang / Vanja Perčulija / Abdullah F U H Saeed / Yichang Liu / Jinyu Li / Syed Sajid Jan / Yu Li / Ping Zhu / Songying Ouyang /
Abstract: Coronaviruses (CoV) have caused a number of major epidemics in humans and animals, including the current pandemic of coronavirus disease 2019 (COVID-19), which has brought a renewed focus on the ...Coronaviruses (CoV) have caused a number of major epidemics in humans and animals, including the current pandemic of coronavirus disease 2019 (COVID-19), which has brought a renewed focus on the evolution and interspecies transmission of coronaviruses. Swine acute diarrhea syndrome coronavirus (SADS-CoV), which was recently identified in piglets in southern China, is an alphacoronavirus that originates from the same genus of horseshoe bats as severe acute respiratory syndrome CoV (SARS-CoV) and that was reported to be capable of infecting cells from a broad range of species, suggesting a considerable potential for interspecies transmission. Given the importance of the coronavirus spike (S) glycoprotein in host range determination and viral entry, we report a cryo-electron microscopy (cryo-EM) structure of the SADS-CoV S trimer in the prefusion conformation at a 3.55-Å resolution. Our structure reveals that the SADS-CoV S trimer assumes an intrasubunit quaternary packing mode in which the S1 subunit N-terminal domain (S1-NTD) and the S1 subunit C-terminal domain (S1-CTD) of the same protomer pack together by facing each other in the lying-down state. SADS-CoV S has several distinctive structural features that may facilitate immune escape, such as a relatively compact architecture of the S trimer and epitope masking by glycan shielding. Comparison of SADS-CoV S with the spike proteins of the other coronavirus genera suggested that the structural features of SADS-CoV S are evolutionarily related to those of the spike proteins of the other genera rather than to the spike protein of a typical alphacoronavirus. These data provide new insights into the evolutionary relationship between spike glycoproteins of SADS-CoV and those of other coronaviruses and extend our understanding of their structural and functional diversity. In this article, we report the atomic-resolution prefusion structure of the spike protein from swine acute diarrhea syndrome coronavirus (SADS-CoV). SADS-CoV is a pathogenic alphacoronavirus that was responsible for a large-scale outbreak of fatal disease in pigs and that was reported to be capable of interspecies transmission. We describe the overall structure of the SADS-CoV spike protein and conducted a detailed analysis of its main structural elements. Our results and analyses are consistent with those of previous phylogenetic studies and suggest that the SADS-CoV spike protein is evolutionarily related to the spike proteins of betacoronaviruses, with a strong similarity in S1-NTDs and a marked divergence in S1-CTDs. Moreover, we discuss the possible immune evasion strategies used by the SADS-CoV spike protein. Our study provides insights into the structure and immune evasion strategies of the SADS-CoV spike protein and broadens the understanding of the evolutionary relationships between coronavirus spike proteins of different genera.
History
DepositionMar 3, 2020-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6m39
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30071.png

Downloads & links

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Map

FileDownload / File: emd_30071.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.14791895 - 0.2631118
Average (Standard dev.)0.00026103298 (±0.011568797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z266.240266.240266.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1480.2630.000

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Supplemental data

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Sample components

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Entire : SADS-CoV spike trimer

EntireName: SADS-CoV spike trimer
Components
  • Complex: SADS-CoV spike trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: SADS-CoV spike trimer

SupramoleculeName: SADS-CoV spike trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Swine acute diarrhea syndrome coronavirus

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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: Swine acute diarrhea syndrome coronavirus
Molecular weightTheoretical: 108.920773 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: GCESVDFNLF NTIFSTHRGL SNTTSVITGA YPSTNKSDWS CNTRTGHLSG SGFGIGLYVQ TPREQYQYDG SGAGGYTIAV SPIHVTNLT WELWIHRKWG VNSVVTVRLC RWWQFMSFNS TSHAADAGPT NAFECLINGS YPTHRNTGYM FGVTWYNDLV R IVFPPTVL ...String:
GCESVDFNLF NTIFSTHRGL SNTTSVITGA YPSTNKSDWS CNTRTGHLSG SGFGIGLYVQ TPREQYQYDG SGAGGYTIAV SPIHVTNLT WELWIHRKWG VNSVVTVRLC RWWQFMSFNS TSHAADAGPT NAFECLINGS YPTHRNTGYM FGVTWYNDLV R IVFPPTVL EMQLDGLQWE RVQFNSPVNA GHATRFNVVK DISTVLVETN SGGSVFRYSY CADGFVNGLQ CKLRLFDIPP GV YSNSEVE YPTALYTVVH NMSACPERPD SYCGSNSCPF KRAVFSNCIV NYTTWVNPDQ RDFQHLILPN GKFNPFTECN GLN RIVDGC VPGFVLRVGR GKAVNRTIVT PYLKPYECFG WSWNDNQDSI YDWWIADFVS TGAFVCESNP EAPKTGVCVT YTVE KVTFQ GVLYESNFTF AQYYNLLYVG SQLRYVRILG KVYEVSSCFE ASYDVLYRNN QSFGLLYRSF DCNQLHIKSA RFVDR LLPS HNGTATVLGC LFNASYAPND TMVNCTNPLG DGFCADLLGN VAVRRMTFEK HDTTYVAPVT NERYTEMPLD HQLILT EQF LQTTMPKFSV SCETYICDVS KACKNLLFRY GGFCQKVEAD IRGAGILLDG DVSSLYSTIA AKTSSVVPTT DRFNVSQ FF LPKTQSSANK YESRSAIEDL LFSKIETTGP GFYGDYYNCK KNAIQDLTCA QYHNGILVIP PIMDAETLGM YGGIAAAS V TLGIFGGQAG MATWSVAMAG RLNALGVVQN ALVDDVNKLA NGFNQLTASV SKLALTTSSA LQAIQAVVNQ NAAQVESLV SGITENFGAI STNFKVISQR LDKLEADVQM DRLINGRMNV LQLFVTNYKL KIAELRNTHR YVQSLINECV YAQSLRNGFC GQGLHVLSL MQNAPSGIMF FHYSLIPNNT ITVKTTPGLC ESDELGSKCI VAKDGVLVSA NLSYWQWSPR NLYKPENLTF A NVIAVSRG ANYTTLNKTF DIP

UniProtKB: Spike glycoprotein

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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: 54 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ab initial model using SGD method
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: RELION
FSC plot (resolution estimation)

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