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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
SampleHuman coronavirus 229E spike glycoprotein:
spike glycoprotein / (ligand) x 3
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 Canada
CitationJournal: Elife / Year: 2019
Title: The human coronavirus HCoV-229E S-protein structure and receptor binding.
Authors: Zhijie Li / Aidan C A Tomlinson / Alan H M 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 ...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.
Validation ReportPDB-ID: 6u7h

SummaryFull reportAbout validation report
History
DepositionSep 2, 2019-
Header (metadata) releaseOct 9, 2019-
Map releaseNov 13, 2019-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing 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
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  • 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

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å
1.06 Å/pix.
x 280 pix.
= 296.8 Å
1.06 Å/pix.
x 280 pix.
= 296.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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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Segmentation: #1

Fileemd_20668_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Human coronavirus 229E spike glycoprotein

EntireName: Human coronavirus 229E spike glycoprotein
Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells
Number of components: 5

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Component #1: protein, Human coronavirus 229E spike glycoprotein

ProteinName: Human coronavirus 229E spike glycoprotein
Details: Ectodomain generated by recombinant expression in HEK293 Freestyle cells
Recombinant expression: No
MassTheoretical: 380 kDa
SourceSpecies: Human coronavirus 229E
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, spike glycoprotein

ProteinName: spike glycoprotein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 127.231117 kDa
SourceSpecies: Human coronavirus 229E / Strain: VR-740
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 63 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #4: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #5: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.8 mg/mL / pH: 8
Support film15 micro Ampere
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: OTHER / Temperature: 295 K / Humidity: 100 % / Details: Blot for 13 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 71350
3D reconstructionSoftware: cryoSPARC / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Details: Manual model building was done in COOT and ChimeraX/ISOLDE. A homology model based on PDB:5SZS was used as a reference during model building.
Input PDB model: 5SZS
Chain ID: A
Output model

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