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- EMDB-22889: A 3.4 Angstrom cryo-EM structure of the human coronavirus spike t... -

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Entry
Database: EMDB / ID: EMD-22889
TitleA 3.4 Angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles
Map dataCryo-EM structure of spike trimer computationally derived from vitrified NL63 virus particles
Sample
  • Complex: HCoV-NL63 spike trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNL63 / in situ / Spike trimer / glycosylation sites / single particle cryo-EM / VIRAL 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 / host cell surface receptor binding / 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 NL63
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsZhang K / Li S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129564 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103832 United States
CitationJournal: bioRxiv / Year: 2020
Title: A 3.4-Å cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles.
Authors: Kaiming Zhang / Shanshan Li / Grigore Pintilie / David Chmielewski / Michael F Schmid / Graham Simmons / Jing Jin / Wah Chiu
Abstract: Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild ...Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV and SARS-CoV-2. Here we present the structure of HCoV-NL63 spike (S) trimer at 3.4-Å resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other amino acid positions as well as differences in glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. This structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.
History
DepositionOct 24, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.528
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.528
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kip
  • Surface level: 0.65
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22889.png

Downloads & links

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Map

FileDownload / File: emd_22889.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of spike trimer computationally derived from vitrified NL63 virus particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 Å		1.4 Å/pix.
x 256 pix.
= 358.4 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: 0.528 / Movie #1: 0.528
Minimum - Maximum-1.8482813 - 4.419859
Average (Standard dev.)0.0048863264 (±0.14207682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.8484.4200.005

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Supplemental data

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Mask #1

Fileemd_22889_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_22889_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_22889_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : HCoV-NL63 spike trimer

EntireName: HCoV-NL63 spike trimer
Components
  • Complex: HCoV-NL63 spike trimer
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HCoV-NL63 spike trimer

SupramoleculeName: HCoV-NL63 spike trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Human coronavirus NL63
Molecular weightTheoretical: 600 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: Human coronavirus NL63
Molecular weightTheoretical: 149.954109 KDa
SequenceString: MKLFLILLVL PLASCFFTCN SNANLSMLQL GVPDNSSTIV TGLLPTHWFC ANQSTSVYSA NGFFYIDVGN HRSAFALHTG YYDANQYYI YVTNEIGLNA SVTLKICKFS RNTTFDFLSN ASSSFDCIVN LLFTEQLGAP LGITISGETV RLHLYNVTRT F YVPAAYKL ...String:
MKLFLILLVL PLASCFFTCN SNANLSMLQL GVPDNSSTIV TGLLPTHWFC ANQSTSVYSA NGFFYIDVGN HRSAFALHTG YYDANQYYI YVTNEIGLNA SVTLKICKFS RNTTFDFLSN ASSSFDCIVN LLFTEQLGAP LGITISGETV RLHLYNVTRT F YVPAAYKL TKLSVKCYFN YSCVFSVVNA TVTVNVTTHN GRVVNYTVCD DCNGYTDNIF SVQQDGRIPN GFPFNNWFLL TN GSTLVDG VSRLYQPLRL TCLWPVPGLK SSTGFVYFNA TGSDVNCNGY QHNSVVDVMR YNLNFSANSL DNLKSGVIVF KTL QYDVLF YCSNSSSGVL DTTIPFGPSS QPYYCFINST INTTHVSTFV GILPPTVREI VVARTGQFYI NGFKYFDLGF IEAV NFNVT TASATDFWTV AFATFVDVLV NVSATNIQNL LYCDSPFEKL QCEHLQFGLQ DGFYSANFLD DNVLPETYVA LPIYY QHTD INFTATASFG GSCYVCKPHQ VNISLNGNTS VCVRTSHFSI RYIYNRVKSG SPGDSSWHIY LKSGTCPFSF SKLNNF QKF KTICFSTVEV PGSCNFPLEA TWHYTSYTIV GALYVTWSEG NSITGVPYPV SGIREFSNLV LNNCTKYNIY DYVGTGI IR SSNQSLAGGI TYVSNSGNLL GFKNVSTGNI FIVTPCNQPD QVAVYQQSII GAMTAVNESR YGLQNLLQLP NFYYVSNG G NNCTTAVMTY SNFGICADGS LIPVRPRNSS DNGISAIITA NLSIPSNWTT SVQVEYLQIT STPIVVDCAT YVCNGNPRC KNLLKQYTSA CKTIEDALRL SAHLETNDVS SMLTFDSNAF SLANVTSFGD YNLSSVLPQR NIRSSRIAGR SALEDLLFSK VVTSGLGTV DVDYKSCTKG LSIADLACAQ YYNGIMVLPG VADAERMAMY TGSLIGGMVL GGLTSAAAIP FSLALQARLN Y VALQTDVL QENQKILAAS FNKAINNIVA SFSSVNDAIT QTAEAIHTVT IALNKIQDVV NQQGSALNHL TSQLRHNFQA IS NSIQAIY DRLDSIQADQ QVDRLITGRL AALNAFVSQV LNKYTEVRGS RRLAQQKINE CVKSQSNRYG FCGNGTHIFS IVN SAPDGL LFLHTVLLPT DYKNVKAWSG ICVDGIYGYV LRQPNLVLYS DNGVFRVTSR VMFQPRLPVL SDFVQIYNCN VTFV NISRV ELHTVIPDYV DVNKTLQEFA QNLPKYVKPN FDLTPFNLTY LNLSSELKQL EAKTASLFQT TVELQGLIDQ INSTY VDLK LLNRFENYIK WPWWVWLIIS VVFVVLLSLL VFCCLSTGCC GCCNCLTSSM RGCCDCGSTK LPYYEFEKVH VQ

UniProtKB: Spike glycoprotein

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 24 / 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

Concentration4.5 mg/mL
BufferpH: 8 / Details: 20 mM Tris, pH 8.0, 120 mM NaCl, 1 mM EDTA
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
DetailsHCoV-NL63 virions

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4138 / Average exposure time: 3.0 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.6 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 64000
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: 944822
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 82030
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

5szs


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: OTHER / Target criteria: Q-score
Output model

PDB-7kip:
A 3.4 Angstrom cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles

PDB-8fr7:
A hinge glycan regulates spike bending and impacts coronavirus infectivity

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