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- EMDB-3391: Negative-stain electron microscopy structure of human cytomegalov... -

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Basic information

Entry
Database: EMDB / ID: EMD-3391
TitleNegative-stain electron microscopy structure of human cytomegalovirus gHgLgO trimer
Map dataThe correct handedness for this complex was unknown at the time of deposition
Sample
  • Sample: Human cytomegalovirus gHgLgO trimer
  • Protein or peptide: Envelope glycoprotein H
  • Protein or peptide: Envelope glycoprotein O
  • Protein or peptide: Envelope glycoprotein L
KeywordsgHgLgO / human cytomegalovirus
Function / homology
Function and homology information


viral process / membrane => GO:0016020 / host cell endosome / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus UL74, glycoprotein / Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H ...Herpesvirus UL74, glycoprotein / Herpesvirus UL74, glycoprotein / Herpes UL74 glycoproteins / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Cytomegalovirus glycoprotein L / Betaherpesvirus glycoprotein L (gL) domain profile. / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain
Similarity search - Domain/homology
Envelope glycoprotein L / Envelope glycoprotein H / Envelope glycoprotein O
Similarity search - Component
Biological speciesHuman herpesvirus 5
Methodsingle particle reconstruction / negative staining / Resolution: 19.3 Å
AuthorsKabanova A / Marcandalli J / Zhou T / Bianchi S / Baxa U / Tsybovsky Y / Lilleri D / Silacci-Fregni C / Foglierini M / Fernandez-Rodriguez BM ...Kabanova A / Marcandalli J / Zhou T / Bianchi S / Baxa U / Tsybovsky Y / Lilleri D / Silacci-Fregni C / Foglierini M / Fernandez-Rodriguez BM / Druz A / Zhang B / Geiger R / Pagani M / Sallusto F / Kwong PD / Corti D / Lanzavecchia A / Perez L
CitationJournal: Nat Microbiol / Year: 2016
Title: Platelet-derived growth factor-α receptor is the cellular receptor for human cytomegalovirus gHgLgO trimer.
Authors: Anna Kabanova / Jessica Marcandalli / Tongqing Zhou / Siro Bianchi / Ulrich Baxa / Yaroslav Tsybovsky / Daniele Lilleri / Chiara Silacci-Fregni / Mathilde Foglierini / Blanca Maria Fernandez- ...Authors: Anna Kabanova / Jessica Marcandalli / Tongqing Zhou / Siro Bianchi / Ulrich Baxa / Yaroslav Tsybovsky / Daniele Lilleri / Chiara Silacci-Fregni / Mathilde Foglierini / Blanca Maria Fernandez-Rodriguez / Aliaksandr Druz / Baoshan Zhang / Roger Geiger / Massimiliano Pagani / Federica Sallusto / Peter D Kwong / Davide Corti / Antonio Lanzavecchia / Laurent Perez /
Abstract: Human cytomegalovirus encodes at least 25 membrane glycoproteins that are found in the viral envelope(1). While gB represents the fusion protein, two glycoprotein complexes control the tropism of the ...Human cytomegalovirus encodes at least 25 membrane glycoproteins that are found in the viral envelope(1). While gB represents the fusion protein, two glycoprotein complexes control the tropism of the virus: the gHgLgO trimer is involved in the infection of fibroblasts, and the gHgLpUL128L pentamer is required for infection of endothelial, epithelial and myeloid cells(2-5). Two reports suggested that gB binds to ErbB1 and PDGFRα (refs 6,7); however, these results do not explain the tropism of the virus and were recently challenged(8,9). Here, we provide a 19 Å reconstruction for the gHgLgO trimer and show that it binds with high affinity through the gO subunit to PDGFRα, which is expressed on fibroblasts but not on epithelial cells. We also provide evidence that the trimer is essential for viral entry in both fibroblasts and epithelial cells. Furthermore, we identify the pentamer, which is essential for infection of epithelial cells, as a trigger for the ErbB pathway. These findings help explain the broad tropism of human cytomegalovirus and indicate that PDGFRα and the viral gO subunit could be targeted by novel anti-viral therapies.
History
DepositionMar 16, 2016-
Header (metadata) releaseMar 23, 2016-
Map releaseJul 13, 2016-
UpdateJun 6, 2018-
Current statusJun 6, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3391.tif

Downloads & links

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Map

FileDownload / File: emd_3391.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe correct handedness for this complex was unknown at the time of deposition
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.22 Å/pix.
x 160 pix.
= 355.2 Å		2.22 Å/pix.
x 160 pix.
= 355.2 Å		2.22 Å/pix.
x 160 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.03685422 - 0.09676909
Average (Standard dev.)-0.00000286 (±0.00604573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.222.222.22
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z355.200355.200355.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0370.097-0.000

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Supplemental data

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Sample components

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Entire : Human cytomegalovirus gHgLgO trimer

EntireName: Human cytomegalovirus gHgLgO trimer
Components
  • Sample: Human cytomegalovirus gHgLgO trimer
  • Protein or peptide: Envelope glycoprotein H
  • Protein or peptide: Envelope glycoprotein O
  • Protein or peptide: Envelope glycoprotein L

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Supramolecule #1000: Human cytomegalovirus gHgLgO trimer

SupramoleculeName: Human cytomegalovirus gHgLgO trimer / type: sample / ID: 1000 / Oligomeric state: Heterotrimer (one gH + one gL + one gO) / Number unique components: 3
Molecular weightExperimental: 390 KDa / Theoretical: 170 KDa / Method: Size exclusion chromatography

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Macromolecule #1: Envelope glycoprotein H

MacromoleculeName: Envelope glycoprotein H / type: protein_or_peptide / ID: 1 / Name.synonym: gH, UL75 / Number of copies: 1 / Oligomeric state: Heterotrimeric with gL and gO / Recombinant expression: Yes
Source (natural)Organism: Human herpesvirus 5 / Strain: VR1814 / synonym: HCMV
Molecular weightTheoretical: 85 KDa
Recombinant expressionOrganism: Chinese Hamster Ovary cells / Recombinant cell: CHO K1SV / Recombinant plasmid: PEE.12.4 and PEE6.4
SequenceUniProtKB: Envelope glycoprotein H / GO: membrane, membrane => GO:0016020, viral envelope / InterPro: Herpesvirus glycoprotein H

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Macromolecule #2: Envelope glycoprotein O

MacromoleculeName: Envelope glycoprotein O / type: protein_or_peptide / ID: 2 / Name.synonym: gO, UL74 / Number of copies: 1 / Oligomeric state: Heterotrimeric with gL and gH / Recombinant expression: Yes
Source (natural)Organism: Human herpesvirus 5 / Strain: VR1814 / synonym: HCMV
Molecular weightTheoretical: 54 KDa
Recombinant expressionOrganism: Chinese Hamster Ovary cells / Recombinant cell: CHO K1SV / Recombinant plasmid: PEE.12.4 and PEE6.4
SequenceUniProtKB: Envelope glycoprotein O / GO: viral envelope / InterPro: Herpesvirus UL74, glycoprotein

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Macromolecule #3: Envelope glycoprotein L

MacromoleculeName: Envelope glycoprotein L / type: protein_or_peptide / ID: 3 / Name.synonym: gL, UL115 / Number of copies: 1 / Oligomeric state: Heterotrimeric with gH and gO / Recombinant expression: Yes
Source (natural)Organism: Human herpesvirus 5 / Strain: VR1814 / synonym: HCMV
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Chinese Hamster Ovary cells / Recombinant cell: CHO K1SV / Recombinant plasmid: PEE.12.4 and PEE6.4
SequenceUniProtKB: Envelope glycoprotein L / GO: viral process, viral envelope / InterPro: Cytomegalovirus glycoprotein L

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES, 150 mM NaCl
StainingType: NEGATIVE
Details: The complex was adsorbed to freshly glow-discharged carbon-coated grids for 15 s, washed with a buffer containing 20 mM HEPES, pH 7.5, and 150 mM NaCl, and stained in several drops of 0.7% uranyl formate
GridDetails: 200 mesh copper grid with carbon support, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateJun 18, 2015
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Number real images: 304
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000
Sample stageSpecimen holder: Room temperature / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

DetailsThe dataset was subjected to iterative stable alignment and clustering (ISAC) in SPARX. The ISAC classes were then used to generate an initial 3D map in EMAN2, which was used as the initial model for three-dimensional reconstruction and refinement using reference projections in SPIDER.
CTF correctionDetails: Each defocus group
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.3 Å / Resolution method: OTHER / Software - Name: SPARX, EMAN2, SPIDER / Number images used: 10356
Final two d classificationNumber classes: 37

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