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- EMDB-8884: RCT reconstruction of HCMV Pentamer with receptor and 3G16 Fab fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-8884
TitleRCT reconstruction of HCMV Pentamer with receptor and 3G16 Fab fragment.
Map dataRCT reconstruction of CMV Pentamer bound to Receptor and 3G16 Fab fragment.
Sample
  • Complex: HCMV Pentamer with receptor and 3G16 Fab fragment bound.
Biological speciesHuman cytomegalovirus
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsCiferri C / Arthur CP / Dosey AM
CitationJournal: Cell / Year: 2018
Title: An Unbiased Screen for Human Cytomegalovirus Identifies Neuropilin-2 as a Central Viral Receptor.
Authors: Nadia Martinez-Martin / Jessica Marcandalli / Christine S Huang / Christopher P Arthur / Michela Perotti / Mathilde Foglierini / Hoangdung Ho / Annie M Dosey / Stephanie Shriver / Jian ...Authors: Nadia Martinez-Martin / Jessica Marcandalli / Christine S Huang / Christopher P Arthur / Michela Perotti / Mathilde Foglierini / Hoangdung Ho / Annie M Dosey / Stephanie Shriver / Jian Payandeh / Alexander Leitner / Antonio Lanzavecchia / Laurent Perez / Claudio Ciferri /
Abstract: Characterizing cell surface receptors mediating viral infection is critical for understanding viral tropism and developing antiviral therapies. Nevertheless, due to challenges associated with ...Characterizing cell surface receptors mediating viral infection is critical for understanding viral tropism and developing antiviral therapies. Nevertheless, due to challenges associated with detecting protein interactions on the cell surface, the host receptors of many human pathogens remain unknown. Here, we build a library consisting of most single transmembrane human receptors and implement a workflow for unbiased and high-sensitivity detection of receptor-ligand interactions. We apply this technology to elucidate the long-sought receptor of human cytomegalovirus (HCMV), the leading viral cause of congenital birth defects. We identify neuropilin-2 (Nrp2) as the receptor for HCMV-pentamer infection in epithelial/endothelial cells and uncover additional HCMV interactors. Using a combination of biochemistry, cell-based assays, and electron microscopy, we characterize the pentamer-Nrp2 interaction and determine the architecture of the pentamer-Nrp2 complex. This work represents an important approach to the study of host-pathogen interactions and provides a framework for understanding HCMV infection, neutralization, and the development of novel anti-HCMV therapies.
History
DepositionAug 9, 2017-
Header (metadata) releaseOct 25, 2017-
Map releaseNov 28, 2018-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: RCSB / 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 radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8884.png

Downloads & links

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Map

FileDownload / File: emd_8884.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRCT reconstruction of CMV Pentamer bound to Receptor and 3G16 Fab fragment.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.4 Å/pix.
x 110 pix.
= 594. Å		5.4 Å/pix.
x 110 pix.
= 594. Å		5.4 Å/pix.
x 110 pix.
= 594. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.08459047 - 0.12333338
Average (Standard dev.)-0.00008147499 (±0.005749341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 594.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z594.000594.000594.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS110110110
D min/max/mean-0.0850.123-0.000

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Supplemental data

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Sample components

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Entire : HCMV Pentamer with receptor and 3G16 Fab fragment bound.

EntireName: HCMV Pentamer with receptor and 3G16 Fab fragment bound.
Components
  • Complex: HCMV Pentamer with receptor and 3G16 Fab fragment bound.

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Supramolecule #1: HCMV Pentamer with receptor and 3G16 Fab fragment bound.

SupramoleculeName: HCMV Pentamer with receptor and 3G16 Fab fragment bound.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human cytomegalovirus
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Hek293

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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

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Number images used: 570
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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