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

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Entry
Database: EMDB / ID: 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.
SampleHCMV Pentamer with receptor and 3G16 Fab fragment bound.:
SourceHuman cytomegalovirus (Human cytomegalovirus)
Methodsingle particle reconstruction / 25 Å resolution
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 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.
DateDeposition: Aug 9, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Nov 28, 2018 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8884.map.gz (map file in CCP4 format, 5325 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
110 pix
5.4 Å/pix.
= 594. Å
110 pix
5.4 Å/pix.
= 594. Å
110 pix
5.4 Å/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
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.08459047 - 0.12333338
Average (Standard dev.)-0.00008147499 (0.005749341)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions110110110
Origin0.00.00.0
Limit109.0109.0109.0
Spacing110110110
CellA=B=C: 594.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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.
Number of components: 1

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Component #1: protein, HCMV Pentamer with receptor and 3G16 Fab fragment bound.

ProteinName: HCMV Pentamer with receptor and 3G16 Fab fragment bound.
Recombinant expression: No
SourceSpecies: Human cytomegalovirus (Human cytomegalovirus)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: Hek293

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7.5
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 1000 (2k x 2k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 570
3D reconstructionResolution: 25 Å / Resolution method: OTHER

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