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- EMDB-5759: Hepatitis C Virus E2 Envelope Glycoprotein Core Structure -

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Basic information

Entry
Database: EMDB / ID: EMD-5759
TitleHepatitis C Virus E2 Envelope Glycoprotein Core Structure
Map dataE2 glycoprotein bound to AR3A Fab, EMAN1 common lines reconstruction
Sample
  • Sample: E2 glycoprotein bound to AR3A Fab
  • Protein or peptide: E2 envelope glycoprotein
  • Protein or peptide: Antigen-binding fragment of antibody AR3A
Keywordshepatitis C / virus / envelope / glycoprotein
Biological speciesHepatitis C virus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 16.0 Å
AuthorsNieusma T / Kong L / Giang E / Kadam RU / Cogburn KE / Hua Y / Dai X / Stanfield RL / Burton DR / Wilson IA ...Nieusma T / Kong L / Giang E / Kadam RU / Cogburn KE / Hua Y / Dai X / Stanfield RL / Burton DR / Wilson IA / Law M / Ward AB
CitationJournal: Science / Year: 2013
Title: Hepatitis C virus E2 envelope glycoprotein core structure.
Authors: Leopold Kong / Erick Giang / Travis Nieusma / Rameshwar U Kadam / Kristin E Cogburn / Yuanzi Hua / Xiaoping Dai / Robyn L Stanfield / Dennis R Burton / Andrew B Ward / Ian A Wilson / Mansun Law /
Abstract: Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host ...Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structures differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.
History
DepositionSep 27, 2013-
Header (metadata) releaseOct 23, 2013-
Map releaseDec 11, 2013-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.54
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.54
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5759_1.png

Downloads & links

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Map

FileDownload / File: emd_5759.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE2 glycoprotein bound to AR3A Fab, EMAN1 common lines reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 120 pix.
= 246. Å		2.05 Å/pix.
x 120 pix.
= 246. Å		2.05 Å/pix.
x 120 pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.54 / Movie #1: 2.54
Minimum - Maximum-4.64416122 - 17.26858902
Average (Standard dev.)0.0 (±0.87834269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-29-29-29
Dimensions120120120
Spacing120120120
CellA=B=C: 246.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-29-29-29
NC/NR/NS120120120
D min/max/mean-4.64417.2690.000

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Supplemental data

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Sample components

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Entire : E2 glycoprotein bound to AR3A Fab

EntireName: E2 glycoprotein bound to AR3A Fab
Components
  • Sample: E2 glycoprotein bound to AR3A Fab
  • Protein or peptide: E2 envelope glycoprotein
  • Protein or peptide: Antigen-binding fragment of antibody AR3A

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Supramolecule #1000: E2 glycoprotein bound to AR3A Fab

SupramoleculeName: E2 glycoprotein bound to AR3A Fab / type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 96 KDa

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Macromolecule #1: E2 envelope glycoprotein

MacromoleculeName: E2 envelope glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: E2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Hepatitis C virus
Molecular weightTheoretical: 46 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T / Recombinant plasmid: pCMV-Tag4A-tpa

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Macromolecule #2: Antigen-binding fragment of antibody AR3A

MacromoleculeName: Antigen-binding fragment of antibody AR3A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 50 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pComb3H

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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

StainingType: NEGATIVE / Details: negative stain with uranyl formate
GridDetails: 400 mesh copper
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
TemperatureAverage: 298 K
DateApr 15, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 439
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected using automatic (difference-of-Gaussians) picking followed by reference-free classification to eliminate noisy picks or non-target aggregation states.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Appion, Spider, Xmipp, Eman1 / Number images used: 29957

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