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- EMDB-10649: Cryo-EM structure of the prefusion state of canine distemper viru... -

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Basic information

Entry
Database: EMDB / ID: EMD-10649
TitleCryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain
Map data
Sample
  • Complex: Canine distemper virus fusion protein
    • Protein or peptide: Fusion glycoprotein F2
    • Protein or peptide: Fusion glycoprotein F1
Keywordsfusion protein / prefusion state / VIRAL PROTEIN
Function / homology
Function and homology information


fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0 / Fusion glycoprotein F0
Similarity search - Component
Biological speciesCanine morbillivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKalbermatter D / Fotiadis D
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationSinergia, Ref. No. 183481 Switzerland
CitationJournal: J Struct Biol X / Year: 2020
Title: Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain.
Authors: David Kalbermatter / Neeta Shrestha / Flavio M Gall / Marianne Wyss / Rainer Riedl / Philippe Plattet / Dimitrios Fotiadis /
Abstract: Measles virus (MeV) and canine distemper virus (CDV), two members of the genus, are still causing important global diseases of humans and animals, respectively. To enter target cells, ...Measles virus (MeV) and canine distemper virus (CDV), two members of the genus, are still causing important global diseases of humans and animals, respectively. To enter target cells, morbilliviruses rely on an envelope-anchored machinery, which is composed of two interacting glycoproteins: a tetrameric receptor binding (H) protein and a trimeric fusion (F) protein. To execute membrane fusion, the F protein initially adopts a metastable, prefusion state that refolds into a highly stable postfusion conformation as the result of a finely coordinated activation process mediated by the H protein. Here, we employed cryo-electron microscopy (cryo-EM) and single particle reconstruction to elucidate the structure of the prefusion state of the CDV F protein ectodomain (solF) at 4.3 Å resolution. Stabilization of the prefusion solF trimer was achieved by fusing the GCNt trimerization sequence at the C-terminal protein region, and expressing and purifying the recombinant protein in the presence of a morbilliviral fusion inhibitor class compound. The three-dimensional cryo-EM map of prefusion CDV solF in complex with the inhibitor clearly shows density for the ligand at the protein binding site suggesting common mechanisms of membrane fusion activation and inhibition employed by different morbillivirus members.
History
DepositionJan 30, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseJul 22, 2020-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xye
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10649.png

Downloads & links

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Map

FileDownload / File: emd_10649.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 160 pix.
= 163.36 Å		1.02 Å/pix.
x 160 pix.
= 163.36 Å		1.02 Å/pix.
x 160 pix.
= 163.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.021 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.054617725 - 0.075741984
Average (Standard dev.)0.00048568187 (±0.0038229106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 163.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0211.0211.021
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z163.360163.360163.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0550.0760.000

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Supplemental data

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Half map: half map 1

Fileemd_10649_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 2

Fileemd_10649_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Canine distemper virus fusion protein

EntireName: Canine distemper virus fusion protein
Components
  • Complex: Canine distemper virus fusion protein
    • Protein or peptide: Fusion glycoprotein F2
    • Protein or peptide: Fusion glycoprotein F1

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Supramolecule #1: Canine distemper virus fusion protein

SupramoleculeName: Canine distemper virus fusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Canine morbillivirus

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Macromolecule #1: Fusion glycoprotein F2

MacromoleculeName: Fusion glycoprotein F2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Canine morbillivirus
Molecular weightTheoretical: 10.128781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QIHWNNLSTI GIIGTDSVHY KIMTRPSHQY LVIKLMPNVS LIDNCTKAEL GEYEKLLNSV LEPINQALTL MTKNVKPLQS VGSGRRQRR

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Fusion glycoprotein F1

MacromoleculeName: Fusion glycoprotein F1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Canine morbillivirus
Molecular weightTheoretical: 47.511637 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FAGVVLAGAA LGVATAAQIT AGIALHQSNL NAQAIQSLRT SLEQSNKAIE EIREATQETV IAVQGVQDYV NNELVPAMQH MSCELVGQR LGLKLLRYYT ELLSIFGPSL RDPISAEISI QALSYALGGE IHKILEKLGY SGNDMIAILE SRGIKTKITH V DLPGKLII ...String:
FAGVVLAGAA LGVATAAQIT AGIALHQSNL NAQAIQSLRT SLEQSNKAIE EIREATQETV IAVQGVQDYV NNELVPAMQH MSCELVGQR LGLKLLRYYT ELLSIFGPSL RDPISAEISI QALSYALGGE IHKILEKLGY SGNDMIAILE SRGIKTKITH V DLPGKLII LSISYPTLSE VKGVIVHRLE AVSYNIGSQE WYTTVPRYVA TNGYLISNFD ESPCVFVSES AICSQNSLYP MS PLLQQCI RGDTSSCART LVSGTMGNKF ILSKGNIVAN CASILCKCYS TGTIINQSPD KLLTFIASDT CPLVEIDGVT IQV GGRQYP DMVYESKVAL GPAISLERLD VGTNLGNALK KLDDAKVLID SSNQILETVR RSSFNFGSLL SVPILICTAL ALLL LIYCC KRRYQQTLKQ NAKVDPTFKP DLTGTSKSYV RSL

UniProtKB: Fusion glycoprotein F0

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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

Concentration0.23 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTRIS2-Amino-2-hydroxymethyl-propane-1,3-diol
100.0 mMNaClsodium chloride
0.1 mMEDTA2,2',2'',2'''-(Ethane-1,2-diyldinitrilo)tetraacetic acid
0.075 mM3GN-(3-cyanophenyl)-2-phenylacetamide
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / 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

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1604 / Average electron dose: 73.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 491315
Startup modelType of model: NONE
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 115248
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 200 / Avg.num./class: 1034 / Software - Name: RELION (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5yzc

chain_id: A, residue_range: 24-104, source_name: PDB, initial_model_type: experimental model

5yzc

chain_id: B, residue_range: 115-471, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6xye:
Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain

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