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- EMDB-30497: Cryo-EM structures of Alphacoronavirus spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-30497
TitleCryo-EM structures of Alphacoronavirus spike glycoprotein
Map data
Sample
  • Complex: HCoV-229E spike trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAlphacoronavirus / spike glycoprotein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / 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 / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / 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, 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 speciesHuman coronavirus 229E
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsSong X / Shi Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31722056 China
National Natural Science Foundation of China (NSFC)31702249 China
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes.
Authors: Xiyong Song / Yuejun Shi / Wei Ding / Tongxin Niu / Limeng Sun / Yubei Tan / Yong Chen / Jiale Shi / Qiqi Xiong / Xiaojun Huang / Shaobo Xiao / Yanping Zhu / Chongyun Cheng / Zhen F Fu / Zhi- ...Authors: Xiyong Song / Yuejun Shi / Wei Ding / Tongxin Niu / Limeng Sun / Yubei Tan / Yong Chen / Jiale Shi / Qiqi Xiong / Xiaojun Huang / Shaobo Xiao / Yanping Zhu / Chongyun Cheng / Zhen F Fu / Zhi-Jie Liu / Guiqing Peng /
Abstract: Coronaviruses spike (S) glycoproteins mediate viral entry into host cells by binding to host receptors. However, how the S1 subunit undergoes conformational changes for receptor recognition has not ...Coronaviruses spike (S) glycoproteins mediate viral entry into host cells by binding to host receptors. However, how the S1 subunit undergoes conformational changes for receptor recognition has not been elucidated in Alphacoronavirus. Here, we report the cryo-EM structures of the HCoV-229E S trimer in prefusion state with two conformations. The activated conformation may pose the potential exposure of the S1-RBDs by decreasing of the interaction area between the S1-RBDs and the surrounding S1-NTDs and S1-RBDs compared to the closed conformation. Furthermore, structural comparison of our structures with the previously reported HCoV-229E S structure showed that the S trimers trended to open the S2 subunit from the closed conformation to open conformation, which could promote the transition from pre- to postfusion. Our results provide insights into the mechanisms involved in S glycoprotein-mediated Alphacoronavirus entry and have implications for vaccine and therapeutic antibody design.
History
DepositionSep 3, 2020-
SupersessionDec 23, 2020ID: EMD-9745
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7cyd
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30497.png

Downloads & links

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Map

FileDownload / File: emd_30497.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.4 Å/pix.
x 200 pix.
= 280. Å		1.4 Å/pix.
x 200 pix.
= 280. Å		1.4 Å/pix.
x 200 pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-10.870193 - 23.497710999999999
Average (Standard dev.)0.000000000012522 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-10.87023.4980.000

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Supplemental data

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Sample components

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Entire : HCoV-229E spike trimer

EntireName: HCoV-229E spike trimer
Components
  • Complex: HCoV-229E spike trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCoV-229E spike trimer

SupramoleculeName: HCoV-229E spike trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus 229E

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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: Human coronavirus 229E
Molecular weightTheoretical: 122.402008 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MFVLLVAYAL LHIAGCQTTN GLNTSYSVCN GCVGYSENVF AVESGGYIPS DFAFNNWFLL TNTSSVVDGV VRSFQPLLLN CLWSVSGLR FTTGFVYFNG TGRGDCKGFS SDVLSDVIRY NLNFEENLRR GTILFKTSYG VVVFYCTNNT LVSGDAHIPF G TVLGNFYC ...String:
MFVLLVAYAL LHIAGCQTTN GLNTSYSVCN GCVGYSENVF AVESGGYIPS DFAFNNWFLL TNTSSVVDGV VRSFQPLLLN CLWSVSGLR FTTGFVYFNG TGRGDCKGFS SDVLSDVIRY NLNFEENLRR GTILFKTSYG VVVFYCTNNT LVSGDAHIPF G TVLGNFYC FVNTTIGNET TSAFVGALPK TVREFVISRT GHFYINGYRY FTLGNVEAVN FNVTTAETTD FCTVALASYA DV LVNVSQT SIANIIYCNS VINRLRCDQL SFDVPDGFYS TSPIQSVELP VSIVSLPVYH KHTFIVLYVD FKPQSGGGKC FNC YPAGVN ITLANFNETK GPLCVDTSHF TTKYVAVYAN VGRWSASINT GNCPFSFGKV NNFVKFGSVC FSLKDIPGGC AMPI VANWA YSKYYTIGSL YVSWSDGDGI TGVPQPVEGV SSFMNVTLDK CTKYNIYDVS GVGVIRVSND TFLNGITYTS TSGNL LGFK DVTKGTIYSI TPCNPPDQLV VYQQAVVGAM LSENFTSYGF SNVVELPKFF YASNGTYNCT DAVLTYSSFG VCADGS IIA VQPRNVSYDS VSAIVTANLS IPSNWTTSVQ VEYLQITSTP IVVDCSTYVC NGNVRCVELL KQYTSACKTI EDALRNS AM LESADVSEML TFDKKAFTLA NVSSFGDYNL SSVIPSLPRS GSRVAGRSAI EDILFSKLVT SGLGTVDADY KKCTKGLS I ADLACAQYYN GIMVLPGVAD AERMAMYTGS LIGGIALGGL TSAASIPFSL AIQSRLNYVA LQTDVLQENQ KILAASFNK AMTNIVDAFT GVNDAITQTS QALQTVATAL NKIQDVVNQQ GNSLNHLTSQ LRQNFQAISS SIQAIYDRLD IIQADQQVDR LITGRLAAL NVFVSHTLTK YTEVRASRQL AQQKVNECVK SQSKRYGFCG NGTHIFSLVN AAPEGLVFLH TVLLPTQYKD V EAWSGLCV DGRNGYVLRQ PNLALYKEGN YYRITSRIMF EPRIPTIADF VQIENCNVTF VNISRSELQT IVPEYIDVNK TL QELSYKL PNYTVPDLVV EQYNQTILNL TSEISTLENK SAELNYTVQK LQTLIDNINS TLVDLKWLNR VETYIKWPW

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: 42 / 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

Concentration0.75 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
10.0 mMC8H18N2O4SHEPES
500.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 5.0 mrad
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Scanner: OTHER / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 2.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 18000
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: 403347
Startup modelType of model: EMDB MAP
EMDB ID:

8331

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2.14.2) / Number images used: 55513
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v2.14.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. v2.14.2)

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Atomic model buiding 1

Initial modelPDB ID:

5szs


Chain - Chain ID: A / Chain - Residue range: 17-1012 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 100 / Target criteria: Correlation coefficient
Output model

PDB-7cyd:
Cryo-EM structures of Alphacoronavirus spike glycoprotein

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