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- EMDB-7631: Cryo-electron microscopy structure of infectious bronchitis coron... -

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Basic information

Entry
Database: EMDB / ID: EMD-7631
TitleCryo-electron microscopy structure of infectious bronchitis coronavirus spike protein
Map dataInfectious bronchitis coronavirus spike protein
Sample
  • Complex: homotrimer of infectious bronchitis coronavirus spike ectodomain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


: / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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
Similarity search - Function
: / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesInfectious bronchitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsShang J / Zheng Y / Yang Y / Liu C / Geng Q / Luo C / Zhang W / Li F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI089728 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI110700 United States
CitationJournal: PLoS Pathog / Year: 2018
Title: Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins.
Authors: Jian Shang / Yuan Zheng / Yang Yang / Chang Liu / Qibin Geng / Chuming Luo / Wei Zhang / Fang Li /
Abstract: As cell-invading molecular machinery, coronavirus spike proteins pose an evolutionary conundrum due to their high divergence. In this study, we determined the cryo-EM structure of avian infectious ...As cell-invading molecular machinery, coronavirus spike proteins pose an evolutionary conundrum due to their high divergence. In this study, we determined the cryo-EM structure of avian infectious bronchitis coronavirus (IBV) spike protein from the γ-genus. The trimeric IBV spike ectodomain contains three receptor-binding S1 heads and a trimeric membrane-fusion S2 stalk. While IBV S2 is structurally similar to those from the other genera, IBV S1 possesses structural features that are unique to different other genera, thereby bridging these diverse spikes into an evolutionary spectrum. Specifically, among different genera, the two domains of S1, the N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), diverge from simpler tertiary structures and quaternary packing to more complex ones, leading to different functions of the spikes in receptor usage and membrane fusion. Based on the above structural and functional comparisons, we propose that the evolutionary spectrum of coronavirus spikes follows the order of α-, δ-, γ-, and β-genus. This study has provided insight into the evolutionary relationships among coronavirus spikes and deepened our understanding of their structural and functional diversity.
History
DepositionMar 27, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseApr 18, 2018-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0454
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0454
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6cv0
  • Surface level: 0.0454
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7631.png

Downloads & links

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Map

FileDownload / File: emd_7631.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInfectious bronchitis coronavirus spike protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 324 pix.
= 330.48 Å		1.02 Å/pix.
x 324 pix.
= 330.48 Å		1.02 Å/pix.
x 324 pix.
= 330.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0454 / Movie #1: 0.0454
Minimum - Maximum-0.14730796 - 0.2232441
Average (Standard dev.)0.0003709477 (±0.0060635507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 330.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z330.480330.480330.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS324324324
D min/max/mean-0.1470.2230.000

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Supplemental data

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Sample components

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Entire : homotrimer of infectious bronchitis coronavirus spike ectodomain

EntireName: homotrimer of infectious bronchitis coronavirus spike ectodomain
Components
  • Complex: homotrimer of infectious bronchitis coronavirus spike ectodomain
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: homotrimer of infectious bronchitis coronavirus spike ectodomain

SupramoleculeName: homotrimer of infectious bronchitis coronavirus spike ectodomain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Infectious bronchitis virus
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9

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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: Infectious bronchitis virus
Molecular weightTheoretical: 121.957703 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ALYDSSSYVY YYQSAFRPPN GWHLHGGAYA VVNISSESNN AGSSPGCIVG TIHGGRVVNA SSIAMTAPSS GMAWSSSQFC TAHCNFSDT TVFVTHCYKY DGCPITGMLQ KNFLRVSAMK NGQLFYNLTV SVAKYPTFKS FQCVNNLTSV YLNGDLVYTS N ETTDVTSA ...String:
ALYDSSSYVY YYQSAFRPPN GWHLHGGAYA VVNISSESNN AGSSPGCIVG TIHGGRVVNA SSIAMTAPSS GMAWSSSQFC TAHCNFSDT TVFVTHCYKY DGCPITGMLQ KNFLRVSAMK NGQLFYNLTV SVAKYPTFKS FQCVNNLTSV YLNGDLVYTS N ETTDVTSA GVYFKAGGPI TYKVMREVKA LAYFVNGTAQ DVILCDGSPR GLLACQYNTG NFSDGFYPFI NSSLVKQKFI VY RENSVNT TFTLHNFTFH NETGANPNPS GVQNIQTYQT QTAQSGYYNF NFSFLSSFVY KESNFMYGSY HPSCNFRLET INN GLWFNS LSVSIAYGPL QGGCKQSVFS GRATCCYAYS YGGPSLCKGV YSGELDLNFE CGLLVYVTKS GGSRIQTATE PPVI TRHNY NNITLNTCVD YNIYGRTGQG FITNVTDSAV SYNYLADAGL AILDTSGSID IFVVQGEYGL TYYKVNPCED VNQQF VVSG GKLVGILTSR NETGSQLLEN QFYIKITNGT RRFRRSITEN VANCPYVSYG KFCIKPDGSI ATIVPKQLEQ FVAPLL NVT ENVLIPNSFN LTVTDEYIQT RMDKVQINCL QYVCGNSLDC RDLFQQYGPV CDNILSVVNS IGQKEDMELL NFYSSTK PA GFNTPFLSNV STGEFNISLL LTTPSSPRRR SFIEDLLFTS VESVGLPTDD AYKNCTAGPL GFLKDLACAR EYNGLLVL P PIITAEMQTL YTSSLVASMA FGGITAAGAI PFATQLQARI NHLGITQSLL LKNQEKIAAS FNKAIGRMQE GFRSTSLAL QQIQHVVNKQ NAILTETMAS LNKNFGAISS LIQEIYQQLD AIQANAQVDR LITGRLSSLS VLASAKQAEH IRVSQQRELA TQKINECVK SQSIRYSFCG NGRHVLTIPQ NAPNGIVFIH FSYTPDSFVN VTAIVGFCVK PANASQYAIV PANGRGIFIQ V NGSYYITA RDMYMPRAIT AGDIVTLTSC QANYVSVNKT VITTFVDNDD FDFNDELSKW WNDTKHELPD FDKFNYTVPI LD IDSEIDR IQGVIQGLND SVDIKQIEDK IEEILSKIYH IENEIARIKK LIGEIGGGGS HHHHHHHH

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 39 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 5.366 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

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102471
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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