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- EMDB-10676: Human Coronavirus HKU1 Haemagglutinin-Esterase -

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Basic information

Entry
Database: EMDB / ID: EMD-10676
TitleHuman Coronavirus HKU1 Haemagglutinin-Esterase
Map dataHuman coronavirus-HKU1 haemagglutinin esterase (local resolution filtered map).
Sample
  • Complex: Human Coronavirus HKU1 Haemagglutinin-Esterase
    • Protein or peptide: Hemagglutinin-esterase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


sialate 9-O-acetylesterase activity / sialate 4-O-acetylesterase activity / sialate O-acetylesterase activity / sialate O-acetylesterase / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin-esterase / Haemagglutinin-esterase glycoprotein, haemagglutinin domain / Haemagglutinin-esterase glycoprotein, core / Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein / Hemagglutinin esterase / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin-esterase
Similarity search - Component
Biological speciesHuman coronavirus HKU1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsHurdiss DL / Drulyte I
Citation
Journal: Nat Commun / Year: 2020
Title: Cryo-EM structure of coronavirus-HKU1 haemagglutinin esterase reveals architectural changes arising from prolonged circulation in humans.
Authors: Daniel L Hurdiss / Ieva Drulyte / Yifei Lang / Tatiana M Shamorkina / Matti F Pronker / Frank J M van Kuppeveld / Joost Snijder / Raoul J de Groot /
Abstract: The human betacoronaviruses HKU1 and OC43 (subgenus Embecovirus) arose from separate zoonotic introductions, OC43 relatively recently and HKU1 apparently much longer ago. Embecovirus particles ...The human betacoronaviruses HKU1 and OC43 (subgenus Embecovirus) arose from separate zoonotic introductions, OC43 relatively recently and HKU1 apparently much longer ago. Embecovirus particles contain two surface projections called spike (S) and haemagglutinin-esterase (HE), with S mediating receptor binding and membrane fusion, and HE acting as a receptor-destroying enzyme. Together, they promote dynamic virion attachment to glycan-based receptors, specifically 9-O-acetylated sialic acid. Here we present the cryo-EM structure of the ~80 kDa, heavily glycosylated HKU1 HE at 3.4 Å resolution. Comparison with existing HE structures reveals a drastically truncated lectin domain, incompatible with sialic acid binding, but with the structure and function of the esterase domain left intact. Cryo-EM and mass spectrometry analysis reveals a putative glycan shield on the now redundant lectin domain. The findings further our insight into the evolution and host adaptation of human embecoviruses, and demonstrate the utility of cryo-EM for studying small, heavily glycosylated proteins.
#1: Journal: Biorxiv / Year: 2020
Title: Cryo-EM structure of coronavirus-HKU1 haemagglutinin esterase reveals architectural changes arising from prolonged circulation in humans
Authors: Hurdiss DL / Drulyte I / Lang Y / Shamorkina TM / Pronker MF / van Kuppeveld FJM / Snijder J / de Groot RJ
History
DepositionFeb 19, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0601
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0601
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6y3y
  • Surface level: 0.0601
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10676.png

Downloads & links

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Map

FileDownload / File: emd_10676.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman coronavirus-HKU1 haemagglutinin esterase (local resolution filtered map).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 320 pix.
= 257.6 Å		0.81 Å/pix.
x 320 pix.
= 257.6 Å		0.81 Å/pix.
x 320 pix.
= 257.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.805 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0601 / Movie #1: 0.0601
Minimum - Maximum-0.17708412 - 0.29912442
Average (Standard dev.)-0.0000526704 (±0.005566763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 257.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8050.8050.805
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z257.600257.600257.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1770.299-0.000

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Supplemental data

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Mask #1

Fileemd_10676_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human coronavirus-HKU1 haemagglutinin esterase (Gaussian filtered N-glycan difference...

Fileemd_10676_additional_1.map
AnnotationHuman coronavirus-HKU1 haemagglutinin esterase (Gaussian filtered N-glycan difference map).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human coronavirus-HKU1 haemagglutinin esterase (unsharpened map).

Fileemd_10676_additional_2.map
AnnotationHuman coronavirus-HKU1 haemagglutinin esterase (unsharpened map).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Human coronavirus-HKU1 haemagglutinin esterase (sharpened map).

Fileemd_10676_additional_3.map
AnnotationHuman coronavirus-HKU1 haemagglutinin esterase (sharpened map).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human coronavirus-HKU1 haemagglutinin esterase (half map 2).

Fileemd_10676_half_map_1.map
AnnotationHuman coronavirus-HKU1 haemagglutinin esterase (half map 2).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human coronavirus-HKU1 haemagglutinin esterase (half map 1).

Fileemd_10676_half_map_2.map
AnnotationHuman coronavirus-HKU1 haemagglutinin esterase (half map 1).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Coronavirus HKU1 Haemagglutinin-Esterase

EntireName: Human Coronavirus HKU1 Haemagglutinin-Esterase
Components
  • Complex: Human Coronavirus HKU1 Haemagglutinin-Esterase
    • Protein or peptide: Hemagglutinin-esterase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Human Coronavirus HKU1 Haemagglutinin-Esterase

SupramoleculeName: Human Coronavirus HKU1 Haemagglutinin-Esterase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Dimeric complex
Source (natural)Organism: Human coronavirus HKU1
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightExperimental: 30.777 KDa

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Macromolecule #1: Hemagglutinin-esterase

MacromoleculeName: Hemagglutinin-esterase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: sialate O-acetylesterase
Source (natural)Organism: Human coronavirus HKU1
Molecular weightTheoretical: 40.432648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LAFNEPLNVV SHLNHDWFLF GDSRSDCNHI NNLKIKNFDY LDIHPSLCNN GKISSSAGDS IFKSFHFTRF YNYTGEGDQI IFYEGVNFN PYHRFKCFPN GSNDVWLLNK VRFYRALYSN MAFFRYLTFV DIPYNVSLSK FNSCKSDILS LNNPIFINYS K EVYFTLLG ...String:
LAFNEPLNVV SHLNHDWFLF GDSRSDCNHI NNLKIKNFDY LDIHPSLCNN GKISSSAGDS IFKSFHFTRF YNYTGEGDQI IFYEGVNFN PYHRFKCFPN GSNDVWLLNK VRFYRALYSN MAFFRYLTFV DIPYNVSLSK FNSCKSDILS LNNPIFINYS K EVYFTLLG CSLYLVPLCL FKSNFSQYYY NIDTGSVYGF SNVVYPDLDC IYISLKPGSY KVSTTAPFLS LPTKALCFDK SK QFVPVQV VDSRWNNERA SDISLSVACQ LPYCYFRNSS ANYVGKYDIN HGDSGFISIL SGLLYNVSCI SYYGVFLYDN FTS IWPYYS FGRCPTSSII KHPICVYDSD PLVPR

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / 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 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Trisaminomethane
50.0 mMNaClSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force = 1 Blot time = 5.5 seconds.

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Electron microscopy

MicroscopeTFS KRIOS
DetailsTitan Krios G4 was used with fringe-free imaging and aberration-free image shift.
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 6029 / Average exposure time: 5.6 sec. / Average electron dose: 40.0 e/Å2 / Details: Falcon 4 Direct Electron Detector
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.0 µm / Nominal magnification: 96000
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

DetailsFalcon 4 Direct Electron Detector
Particle selectionNumber selected: 936260 / Details: Relion autopicking
CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: INSILICO MODEL
In silico model: A homology model of the dimeric HCoV-HKU1 HE (uniprot ID: Q5MQD1) was generated using the phyre2 server. The molmap command in UCSF chimera, was then used to create a 40 angstrom ...In silico model: A homology model of the dimeric HCoV-HKU1 HE (uniprot ID: Q5MQD1) was generated using the phyre2 server. The molmap command in UCSF chimera, was then used to create a 40 angstrom resolution starting model.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 119717
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 141000 / Software - Name: RELION (ver. 3.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsA homology model of HCOV-HKU1 HE (uniprot ID: Q5MQD1) was generated using the phyre2 server
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-6y3y:
Human Coronavirus HKU1 Haemagglutinin-Esterase

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