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- EMDB-14842: Cryo-EM structure of the canine distemper virus tetrameric attach... -

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Basic information

Entry
Database: EMDB / ID: EMD-14842
TitleCryo-EM structure of the canine distemper virus tetrameric attachment glycoprotein
Map datafinal sharpened map
Sample
  • Virus: Canine morbillivirus
    • Protein or peptide: Hemagglutinin glycoprotein
Function / homology
Function and homology information


host cell membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin glycoprotein
Similarity search - Component
Biological speciesCanine morbillivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsKalbermatter D / Jeckelmann J-M / Wyss M / Plattet P / Fotiadis D
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationSinergia, Ref. No. 183481 Switzerland
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure and supramolecular organization of the canine distemper virus attachment glycoprotein.
Authors: David Kalbermatter / Jean-Marc Jeckelmann / Marianne Wyss / Neeta Shrestha / Dimanthi Pliatsika / Rainer Riedl / Thomas Lemmin / Philippe Plattet / Dimitrios Fotiadis /
Abstract: Canine distemper virus (CDV) is an enveloped RNA morbillivirus that triggers respiratory, enteric, and high incidence of severe neurological disorders. CDV induces devastating outbreaks in wild and ...Canine distemper virus (CDV) is an enveloped RNA morbillivirus that triggers respiratory, enteric, and high incidence of severe neurological disorders. CDV induces devastating outbreaks in wild and endangered animals as well as in domestic dogs in countries associated with suboptimal vaccination programs. The receptor-binding tetrameric attachment (H)-protein is part of the morbilliviral cell entry machinery. Here, we present the cryo-electron microscopy (cryo-EM) structure and supramolecular organization of the tetrameric CDV H-protein ectodomain. The structure reveals that the morbilliviral H-protein is composed of three main domains: stalk, neck, and heads. The most unexpected feature was the inherent asymmetric architecture of the CDV H-tetramer being shaped by the neck, which folds into an almost 90° bent conformation with respect to the stalk. Consequently, two non-contacting receptor-binding H-head dimers, which are also tilted toward each other, are located on one side of an intertwined four helical bundle stalk domain. Positioning of the four protomer polypeptide chains within the neck domain is guided by a glycine residue (G158), which forms a hinge point exclusively in two protomer polypeptide chains. Molecular dynamics simulations validated the stability of the asymmetric structure under near physiological conditions and molecular docking showed that two receptor-binding sites are fully accessible. Thus, this spatial organization of the CDV H-tetramer would allow for concomitant protein interactions with the stalk and head domains without steric clashes. In summary, the structure of the CDV H-protein ectodomain provides new insights into the morbilliviral cell entry system and offers a blueprint for next-generation structure-based antiviral drug discovery.
History
DepositionApr 23, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 15, 2023-
Current statusFeb 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14842.png

Downloads & links

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Map

FileDownload / File: emd_14842.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 224 pix.
= 289.343 Å		1.29 Å/pix.
x 224 pix.
= 289.343 Å		1.29 Å/pix.
x 224 pix.
= 289.343 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29171 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.65
Minimum - Maximum-3.8715262 - 6.5947504
Average (Standard dev.)0.017903805 (±0.13066565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 289.34305 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14842_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Additional map: full map

Fileemd_14842_additional_1.map
Annotationfull map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_14842_half_map_1.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_14842_half_map_2.map
Annotationhalf map2
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Canine morbillivirus

EntireName: Canine morbillivirus
Components
  • Virus: Canine morbillivirus
    • Protein or peptide: Hemagglutinin glycoprotein

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Supramolecule #1: Canine morbillivirus

SupramoleculeName: Canine morbillivirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11232 / Sci species name: Canine morbillivirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Molecular weightTheoretical: 272 KDa

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Macromolecule #1: Hemagglutinin glycoprotein

MacromoleculeName: Hemagglutinin glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Canine morbillivirus
Molecular weightTheoretical: 68.311031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLSYQDKVSA FYKDNARANS SKLSLVTEEQ GGRRPPYLLF VLLILLVGIM ALLAITGVRF HQVSTSNMEF SRLLKEDMEK SEAVHHQVI DVLTPLFKII GDEIGLRLPQ KLNEIKQFIL QKTNFFNPNR EFDFRDLHWC INPPSKIKVN FTNYCDTIGI R KSIASAAN ...String:
MLSYQDKVSA FYKDNARANS SKLSLVTEEQ GGRRPPYLLF VLLILLVGIM ALLAITGVRF HQVSTSNMEF SRLLKEDMEK SEAVHHQVI DVLTPLFKII GDEIGLRLPQ KLNEIKQFIL QKTNFFNPNR EFDFRDLHWC INPPSKIKVN FTNYCDTIGI R KSIASAAN PILLSALSGG RGDIFPPYRC SGATTSVGRV FPLSVSLSMS LISRTSEIIN MLTAISDGVY GKTYLLVPDY IE GGFDTQK IRVFEIGFIK RWLNDMPLLQ TTNYMVLPEN SKAKVCTIAV GELTLASLCV DESTVLLYHD SDGSQDGILV VTL GIFGAT PMDQVEEVIP VAHPSVEKIH ITNHRGFIKD SIATWMVPAL VSEKQEEQKN CLESACQRKS YPMCNQTSWE PFGG GQLPS YGRLTLPLDP SIDLQLNISF TYGPVILNGD GMDYYESPLL DSGWLTIPPK NGTVLGLINK ASRGDQFTVI PHVLT FAPR ESSGNCYLPI QTSQIMDKDV LTESNLVVLP TQNFRYVIAT YDISRGDHAI VYYVYDPIRA ISYTYPFRLT TKGRPD FLR IECFVWDDDL WCHQFYRFEA DSTNSTTSVE NLVRIRFSCN RSKP

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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

Concentration1.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTRIS2-Amino-2-hydroxymethyl-propane-1,3-diol
100.0 mMNaClSodium chloridesodium chloride
0.1 %OGn-Octyl-beta-d-glucoside
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot Time: 3.5 sec Blot Force: -6 Drain Time: 0 Wait Time: 0.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 20.0 µm / Nominal defocus min: 8.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 26835 / Average exposure time: 1.5 sec. / Average electron dose: 50.0 e/Å2
Details: Two Datasets from two different grids were recorded: 13,760 and 13,075 movies
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6471114
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 294000 / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 663258
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7zny:
Cryo-EM structure of the canine distemper virus tetrameric attachment glycoprotein

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