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- EMDB-30037: Cryo-EM structures of HKU2 spike glycoproteins -

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Basic information

Entry
Database: EMDB / ID: EMD-30037
TitleCryo-EM structures of HKU2 spike glycoproteins
Map data
Sample
  • Complex: HKU2 glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 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 S2 superfamily, coronavirus / 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 / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesRhinolophus bat coronavirus HKU2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsWang X / Yu J / Qiao S / Guo R
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus evolution.
Authors: Jinfang Yu / Shuyuan Qiao / Runyu Guo / Xinquan Wang /
Abstract: Porcine coronavirus SADS-CoV has been identified from suckling piglets with severe diarrhea in southern China in 2017. The SADS-CoV genome shares ~95% identity to that of bat α-coronavirus HKU2, ...Porcine coronavirus SADS-CoV has been identified from suckling piglets with severe diarrhea in southern China in 2017. The SADS-CoV genome shares ~95% identity to that of bat α-coronavirus HKU2, suggesting that SADS-CoV may have emerged from a natural reservoir in bats. Here we report the cryo-EM structures of HKU2 and SADS-CoV spike (S) glycoprotein trimers at 2.38 Å and 2.83 Å resolution, respectively. We systematically compare the domains of HKU2 spike with those of α-, β-, γ-, and δ-coronavirus spikes, showing that the S1 subunit N- and C-terminal domains of HKU2/SADS-CoV are ancestral domains in the evolution of coronavirus spike proteins. The connecting region after the fusion peptide in the S2 subunit of HKU2/SADS-CoV adopts a unique conformation. These results structurally demonstrate a close evolutionary relationship between HKU2/SADS-CoV and β-coronavirus spikes and provide insights into the evolution and cross-species transmission of coronaviruses.
History
DepositionFeb 24, 2020-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6m15
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30037.png

Downloads & links

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Map

FileDownload / File: emd_30037.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.)
1.06 Å/pix.
x 256 pix.
= 271.616 Å		1.06 Å/pix.
x 256 pix.
= 271.616 Å		1.06 Å/pix.
x 256 pix.
= 271.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0201 / Movie #1: 0.03
Minimum - Maximum-0.1313678 - 0.25833428
Average (Standard dev.)0.00039474524 (±0.0075939964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.616271.616271.616
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1310.2580.000

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Supplemental data

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Sample components

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Entire : HKU2 glycoprotein

EntireName: HKU2 glycoprotein
Components
  • Complex: HKU2 glycoprotein
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: HKU2 glycoprotein

SupramoleculeName: HKU2 glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhinolophus bat coronavirus HKU2

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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: Rhinolophus bat coronavirus HKU2
Molecular weightTheoretical: 124.52668 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKLFIVFVLL FRVCYCCDYV DFRLFNGIFS TSRGLSNTTT VITGAYPSTN KAKWFCPTNV GRPVGTGVGI GVYAQTAQAS YETGGSGAG GYTFSVSPKH VTNLTWSLWV HRPWGANANV TVRLCRWWQK FSFNETAHFQ PAGPSSAFEC LVNGSFPSSQ H KGYMFGVT ...String:
MKLFIVFVLL FRVCYCCDYV DFRLFNGIFS TSRGLSNTTT VITGAYPSTN KAKWFCPTNV GRPVGTGVGI GVYAQTAQAS YETGGSGAG GYTFSVSPKH VTNLTWSLWV HRPWGANANV TVRLCRWWQK FSFNETAHFQ PAGPSSAFEC LVNGSFPSSQ H KGYMFGVT WYNDFVRIIF PPTVFELQLD GLQWEYVQFT GPVNAGRMTK FNVVTEISSV LVLTDQSGAV TRYSYCADGF VN GLQCKLR LFDIPPGVYS NSEVEYPVAL YTVVHNMSVC PQRPESYCGS NYCPFKRVVF SNCVVNYTSW TSGLLRDYQH LVL PNGKFN PFTECNGLNR IVDDCVTGFV LRVGRGTAVN RTVITPYLKP NECFGWSWND YQDSIYDWWI ADFVSTGAFV CEKN PDAPR TGVCITYTIE KVTFQGVLYE SNFTFAQYYN VLYFGSQLKY VRILGKVYEV APCFEASYDV LFRSSSSFGL LYRSF DCNQ LRISASRFAE RLLPSHNGTA TALGCLFNAT YAPNDTMVNC TNPLGDGFCA DLLSNVVVRR MTFEKHDTTY VAPVTN ERF TELPLDHQLV LTEQFLQTTM PKFSISCETY ICDVSKACKN LLFRYGGFCQ KIEADIRGAG VLLDSDVSGL YSTIAAK TS SITPTTDRFN VSQFFLPKVQ SNSERFESRS VIEDLLFSKI ETTGPGFYGD YYNCKKNAIQ DLTCAQYHNG ILVIPPVM D AETLGMYGGI AAASLTLGIF GGQAGITTWS LAMAGRLNAL GVVQNALVDD VNKLANGFNQ LTASVGKLAL TTSSALQAI QAVVNQNAAQ VESLVSGITE NFGAISTNFK VISQRLDKLE ADVQMDRLIN GRMNVLQLFV TNYKLKIAEL RNTHRYVQSL INECVYAQS LRNGFCGQGL HVLSLMQNAP SGIMFFHYSL IPNNTITVKT TPGLCESDEL GSKCIVAKDG VLVSANLSYW Q WSPRNLYK PENLTFANVI AVSRGANYTT LNRTFDIPEL NSTFPIDEEF REYFQNMSSE LQALKNLTAD MSKLNISAEI QL INEIAHN VSNMRVEVEK FQRYVNYVKL EVLFQGPGGG SGGGSGYIPE APRDGQAYVR KDGEWVLLST FLGWSHPQFE K

UniProtKB: Spike glycoprotein

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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: 27 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 71 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.3 mg/mL
BufferpH: 7.2
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: 49.784 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: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 421490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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