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- EMDB-6437: RCT reconstruction of CMV protein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6437
TitleRCT reconstruction of CMV protein complex
Map dataRCT reconstruction of CMV protein complex
Sample
  • Sample: RCT reconstruction of CMV Complex bound to neutralizing Fabs
  • Protein or peptide: CMV protein complex
  • Protein or peptide: neutralizing antibody
Biological speciesCytomegalovirus / unidentified (others)
Methodsingle particle reconstruction / Resolution: 30.0 Å
AuthorsCiferri C / Cianfrocco MA / Chandramouli S / Carfi A
CitationJournal: PLoS Pathog / Year: 2015
Title: Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies.
Authors: Claudio Ciferri / Sumana Chandramouli / Alexander Leitner / Danilo Donnarumma / Michael A Cianfrocco / Rachel Gerrein / Kristian Friedrich / Yukti Aggarwal / Giuseppe Palladino / Ruedi ...Authors: Claudio Ciferri / Sumana Chandramouli / Alexander Leitner / Danilo Donnarumma / Michael A Cianfrocco / Rachel Gerrein / Kristian Friedrich / Yukti Aggarwal / Giuseppe Palladino / Ruedi Aebersold / Nathalie Norais / Ethan C Settembre / Andrea Carfi /
Abstract: Human Cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and in fetuses following congenital infection. The glycoprotein complexes gH/gL/gO and ...Human Cytomegalovirus (HCMV) is a major cause of morbidity and mortality in transplant patients and in fetuses following congenital infection. The glycoprotein complexes gH/gL/gO and gH/gL/UL128/UL130/UL131A (Pentamer) are required for HCMV entry in fibroblasts and endothelial/epithelial cells, respectively, and are targeted by potently neutralizing antibodies in the infected host. Using purified soluble forms of gH/gL/gO and Pentamer as well as a panel of naturally elicited human monoclonal antibodies, we determined the location of key neutralizing epitopes on the gH/gL/gO and Pentamer surfaces. Mass Spectrometry (MS) coupled to Chemical Crosslinking or to Hydrogen Deuterium Exchange was used to define residues that are either in proximity or part of neutralizing epitopes on the glycoprotein complexes. We also determined the molecular architecture of the gH/gL/gO- and Pentamer-antibody complexes by Electron Microscopy (EM) and 3D reconstructions. The EM analysis revealed that the Pentamer specific neutralizing antibodies bind to two opposite surfaces of the complex, suggesting that they may neutralize infection by different mechanisms. Together, our data identify the location of neutralizing antibodies binding sites on the gH/gL/gO and Pentamer complexes and provide a framework for the development of antibodies and vaccines against HCMV.
History
DepositionAug 24, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseAug 24, 2016-
UpdateNov 9, 2016-
Current statusNov 9, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6437.jpg

Downloads & links

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Map

FileDownload / File: emd_6437.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRCT reconstruction of CMV protein complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 100 pix.
= 430. Å		4.3 Å/pix.
x 100 pix.
= 430. Å		4.3 Å/pix.
x 100 pix.
= 430. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-4.06964922 - 25.059598919999999
Average (Standard dev.)0.0 (±0.99999952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 430.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.34.34.3
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z430.000430.000430.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-4.07025.060-0.000

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Supplemental data

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Sample components

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Entire : RCT reconstruction of CMV Complex bound to neutralizing Fabs

EntireName: RCT reconstruction of CMV Complex bound to neutralizing Fabs
Components
  • Sample: RCT reconstruction of CMV Complex bound to neutralizing Fabs
  • Protein or peptide: CMV protein complex
  • Protein or peptide: neutralizing antibody

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Supramolecule #1000: RCT reconstruction of CMV Complex bound to neutralizing Fabs

SupramoleculeName: RCT reconstruction of CMV Complex bound to neutralizing Fabs
type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: CMV protein complex

MacromoleculeName: CMV protein complex / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Cytomegalovirus
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #2: neutralizing antibody

MacromoleculeName: neutralizing antibody / type: protein_or_peptide / ID: 2 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
DateJun 1, 2014
Image recordingCategory: CCD / Film or detector model: FEI CETA (4k x 4k)
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Number images used: 2000

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