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- EMDB-20668: Cryo-EM structure of the HCoV-229E spike glycoprotein -

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Basic information

Entry
Database: EMDB / ID: EMD-20668
TitleCryo-EM structure of the HCoV-229E spike glycoprotein
Map data
Sample
  • Complex: Human coronavirus 229E spike glycoprotein
    • Protein or peptide: spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / 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 speciesHuman coronavirus 229E
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi Z / Benlekbir S / Rubinstein JL / Rini JM
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Elife / Year: 2019
Title: The human coronavirus HCoV-229E S-protein structure and receptor binding.
Authors: Zhijie Li / Aidan Ca Tomlinson / Alan Hm Wong / Dongxia Zhou / Marc Desforges / Pierre J Talbot / Samir Benlekbir / John L Rubinstein / James M Rini /
Abstract: The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S- ...The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S-protein function is maintained is not understood. Reported are the X-ray crystal structures of Class III-V RBDs in complex with human aminopeptidase N (hAPN), as well as the electron cryomicroscopy structure of the 229E S-protein. The structures show that common core interactions define the specificity for hAPN and that the peripheral RBD sequence variation is accommodated by loop plasticity. The results provide insight into immune evasion and the cross-species transmission of 229E and related coronaviruses. We also find that the 229E S-protein can expose a portion of its helical core to solvent. This is undoubtedly facilitated by hydrophilic subunit interfaces that we show are conserved among coronaviruses. These interfaces likely play a role in the S-protein conformational changes associated with membrane fusion.
History
DepositionSep 2, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseNov 13, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.26
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.26
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6u7h
  • Surface level: 0.33
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20668.png

Downloads & links

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Map

FileDownload / File: emd_20668.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.26 / Movie #1: 0.26
Minimum - Maximum-1.2540375 - 2.5414875
Average (Standard dev.)0.001460505 (±0.087729774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z296.800296.800296.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-1.2542.5410.001

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Supplemental data

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Mask #1

Fileemd_20668_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_20668_additional.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_20668_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_20668_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human coronavirus 229E spike glycoprotein

EntireName: Human coronavirus 229E spike glycoprotein
Components
  • Complex: Human coronavirus 229E spike glycoprotein
    • Protein or peptide: spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human coronavirus 229E spike glycoprotein

SupramoleculeName: Human coronavirus 229E spike glycoprotein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells
Source (natural)Organism: Human coronavirus 229E
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 380 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 229E / Strain: VR-740
Molecular weightTheoretical: 127.231117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 FVNTTIGTET TSAFVGALPK TVREFVISRT GHFYINGYRY FTLGNVEAVN FNVTTAETTD FFTVALASYA DV LVNVSQT SIANIIYCNS VINRLRCDQL SFYVPDGFYS TSPIQSVELP VSIVSLPVYH KHMFIVLYVD FKPQSGGGKC FNC YPAGVN ITLANFNETK GPLCVDTSHF TTKYVAVYAN VGRWSASINT GNCPFSFGKV NNFVKFGSVC FSLKDIPGGC AMPI VANWA YSKYYTIGTL YVSWSDGDGI TGVPQPVEGV SSFMNVTLDK CTKYNIYDVS GVGVIRVSND TFLNGITYTS TSGNL LGFK DVTKGTIYSI TPCNPPDQLV VYQQAVVGAM LSENFTSYGF SNVVELPKFF YASNGTYNCT DAVLTYSSFG VCADGS IIA VQPRNVSYDS VSAIVTANLS IPSNWTISVQ VEYLQITSTP IVVDCSTYVC NGNVRCVELL KQYTSACKTI EDALRNS AR LESADVSEML TFDKKAFTLA NVSSFGDYNL SSVIPSLPTS GSRVAGRSAI EDILFSKIVT SGLGTVDADY KNCTKGLS I ADLACAQYYN GIMVLPGVAD AERMAMYTGS LIGGIALGGL TSAVSIPFSL AIQARLNYVA LQTDVLQENQ KILAASFNK AMTNIVDAFT GVNDAITQTS QALQTVATAL NKIQDVVNQQ GNSLNHLTSQ LRQNFQAISS SIQAIYDRLD PPQADQQVDR LITGRLAAL NVFVSHTLTK YTEVRASRQL AQQKVNECVK SQSKRYGFCG NGTHIFSIVN AAPEGLVFLH TVLLPTQYKD V EAWSGLCV DGTNGYVLRQ PNLALYKEGN YYRITSRIMF EPRIPTMADF VQIENCNVTF VNISRSELQT IVPEYIDVNK TL QELSYKL PNYTVPDLVV EQYNQTILNL TSEISTLENK SAELNYTVQK LQTLIDNINS TLVDLKWLNR VETYIKSGGY IPE APRDGQ AYVRKDGEWV LLSTFLNSEN LYFQSGSHHH HHH

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 33 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
10.0 mMC4H11NO3Tris
GridMaterial: COPPER / Mesh: 400 / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 3.5 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa / Details: 15 micro Ampere
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Blot for 13 seconds before plunging.
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 60.0 sec. / Average electron dose: 42.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.10)
Startup modelType of model: NONE
Details: A initial 3D map was generated by ab-initio reconstruction in cryoSPARC v2.
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.90) / Number images used: 71350

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Atomic model buiding 1

Initial modelPDB ID:

5szs


Chain - Chain ID: A
DetailsManual model building was done in COOT and ChimeraX/ISOLDE. A homology model based on PDB:5SZS was used as a reference during model building.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6u7h:
Cryo-EM structure of the HCoV-229E spike glycoprotein

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