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- EMDB-1121: Mapping the structure and function of the E1 and E2 glycoproteins... -

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Basic information

Entry
Database: EMDB / ID: EMD-1121
TitleMapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
Map datacenter of virus is where z=0
Sample
  • Sample: Sindbis TE12 E2-N318Q
  • Virus: Sindbis virus
Function / homology
Function and homology information


icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / viral translational frameshifting / serine-type endopeptidase activity ...icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / identical protein binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesSindbis virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 9.0 Å
AuthorsMukhopadhyay S / Zhang W / Gabler S / Chipman PR / Strauss EG / Strauss JH / Baker TS / Kuhn RJ / Rossmann MG
CitationJournal: Structure / Year: 2006
Title: Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
Authors: Suchetana Mukhopadhyay / Wei Zhang / Stefan Gabler / Paul R Chipman / Ellen G Strauss / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann /
Abstract: The 9 A resolution cryo-electron microscopy map of Sindbis virus presented here provides structural information on the polypeptide topology of the E2 protein, on the interactions between the E1 and ...The 9 A resolution cryo-electron microscopy map of Sindbis virus presented here provides structural information on the polypeptide topology of the E2 protein, on the interactions between the E1 and E2 glycoproteins in the formation of a heterodimer, on the difference in conformation of the two types of trimeric spikes, on the interaction between the transmembrane helices of the E1 and E2 proteins, and on the conformational changes that occur when fusing with a host cell. The positions of various markers on the E2 protein established the approximate topology of the E2 structure. The largest conformational differences between the icosahedral surface spikes at icosahedral 3-fold and quasi-3-fold positions are associated with the monomers closest to the 5-fold axes. The long E2 monomers, containing the cell receptor recognition motif at their extremities, are shown to rotate by about 180 degrees and to move away from the center of the spikes during fusion.
History
DepositionApr 8, 2005-
Header (metadata) releaseApr 8, 2005-
Map releaseJan 16, 2006-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 75
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 75
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1z8y
  • Surface level: 100
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2xfb
  • Surface level: 100
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3muw
  • Surface level: 100
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1z8y
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2xfb
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3muw
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1121.gif

Downloads & links

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Map

FileDownload / File: emd_1121.map.gz / Format: CCP4 / Size: 319.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcenter of virus is where z=0
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.78 Å/pix.
x 441 pix.
= 787.18 Å		1.78 Å/pix.
x 441 pix.
= 787.18 Å		1.78 Å/pix.
x 441 pix.
= 787.18 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.78499 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 138.0 / Movie #1: 75
Minimum - Maximum-297.649999999999977 - 402.470000000000027
Average (Standard dev.)7.03224 (±65.091200000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-220-220-220
Dimensions441441441
Spacing441441441
CellA=B=C: 787.18 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.78498866213151.78498866213151.7849886621315
M x/y/z441441441
origin x/y/z0.0000.0000.000
length x/y/z787.180787.180787.180
α/β/γ90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S213
start NC/NR/NS-220-220-220
NC/NR/NS441441441
D min/max/mean-297.650402.4707.032

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Supplemental data

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Sample components

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Entire : Sindbis TE12 E2-N318Q

EntireName: Sindbis TE12 E2-N318Q
Components
  • Sample: Sindbis TE12 E2-N318Q
  • Virus: Sindbis virus

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Supramolecule #1000: Sindbis TE12 E2-N318Q

SupramoleculeName: Sindbis TE12 E2-N318Q / type: sample / ID: 1000
Details: Sample is a single deglycosylated virus. For mutagenesis and purification, please see Pletnev et al. (2001) Cell. Virus contains 3 proteins (E1, E2, capsid), a lipid bilyer, and a positive-strand RNA genome.
Number unique components: 1

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Supramolecule #1: Sindbis virus

SupramoleculeName: Sindbis virus / type: virus / ID: 1 / Name.synonym: Sindbis strain TE12 / Details: deglycosylated virus / NCBI-ID: 11034 / Sci species name: Sindbis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Sindbis strain TE12
Host (natural)Organism: Homo sapiens (human) / synonym: INVERTEBRATES
Molecular weightExperimental: 52 MDa
Virus shellShell ID: 1 / Name: glycoprotein / Diameter: 710 Å / T number (triangulation number): 4
Virus shellShell ID: 2 / Name: lipid bilayer / Diameter: 480 Å / T number (triangulation number): 4
Virus shellShell ID: 3 / Name: capsid / Diameter: 410 Å / T number (triangulation number): 4

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA
StainingType: NEGATIVE / Details: no staining
GridDetails: holey carbon 400 mesh copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Purdue manufactured, gravity driven device. Vitrification carried out in hood.
Timed resolved state: Vitrified immediately after blotting. / Method: standard methods

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Electron microscopy

MicroscopeFEI/PHILIPS CM200T
TemperatureMin: 87 K / Max: 100 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
DetailsLow dose
DateJun 21, 2000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 27 / Average electron dose: 18 e/Å2 / Details: optical density range is 0.33-1.35 / Od range: 1 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39220 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.58 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected interactively at the computer terminal.
CTF correctionDetails: CTF correction of each particle.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Purdue Suite
Details: resolution determined by splitting data set into two groups.
Number images used: 7085
Final angle assignmentDetails: Euler angles (theta, phi, omega) are defined as three successive rotations in a right hand coordinate system. First, the viewer is rotated counterclockwise around the z-axis (angle 'phi') ...Details: Euler angles (theta, phi, omega) are defined as three successive rotations in a right hand coordinate system. First, the viewer is rotated counterclockwise around the z-axis (angle 'phi') and then rotated counterclockwise around the new y-axis (angle 'theta') and rotate clockwise around the new z-axis (angle 'omega').
Final two d classificationNumber classes: 3

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Atomic model buiding 1

Initial modelPDB ID:

1i9w

SoftwareName: EMFIT
DetailsProtocol: Rigid body. each protein in the asymmetric unit was fitting individually.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf
Output model

PDB-1z8y:
Mapping the E2 Glycoprotein of Alphaviruses

PDB-2xfb:
CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SINDBIS VIRUS cryo- EM MAP

PDB-3muw:
Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus

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Atomic model buiding 2

Initial modelPDB ID:

1xyk

SoftwareName: EMFIT
DetailsProtocol: Rigid body. each protein in the asymmetric unit was fitting individually.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: sumf
Output model

PDB-1z8y:
Mapping the E2 Glycoprotein of Alphaviruses

PDB-2xfb:
CHIKUNGUNYA E1 E2 ENVELOPE GLYCOPROTEINS FITTED IN SINDBIS VIRUS cryo- EM MAP

PDB-3muw:
Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus

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