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- PDB-1z8y: Mapping the E2 Glycoprotein of Alphaviruses -

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Basic information

Entry
Database: PDB / ID: 1z8y
TitleMapping the E2 Glycoprotein of Alphaviruses
Components
  • (Spike glycoprotein E1) x 3
  • Capsid protein C
  • Spike glycoprotein E2
KeywordsVIRUS / icosahedral enveloped virus / Icosahedral 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 / membrane => GO:0016020 / 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 / membrane => GO:0016020 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA 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
Similarity search - Component
Biological speciesSindbis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
AuthorsMukhopadhyay, S. / Zhang, W. / Gabler, S. / Chipman, P.R. / Strauss, E.G. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G.
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
DepositionMar 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c
Remark 999SEQUENCE Author states that it appears even though the correct sequence utilizes a lysine, leucine ...SEQUENCE Author states that it appears even though the correct sequence utilizes a lysine, leucine was used in the model.

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1121
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  • Superimposition on EM map
  • EMDB-1121
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein E1
B: Spike glycoprotein E1
C: Spike glycoprotein E1
D: Spike glycoprotein E1
E: Spike glycoprotein E1
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E1
J: Spike glycoprotein E2
K: Spike glycoprotein E1
L: Spike glycoprotein E2
M: Spike glycoprotein E1
N: Spike glycoprotein E2
O: Spike glycoprotein E1
P: Spike glycoprotein E2
Q: Capsid protein C
R: Capsid protein C
S: Capsid protein C
T: Capsid protein C


Theoretical massNumber of molelcules
Total (without water)258,38320
Polymers258,38320
Non-polymers00
Water0
1
A: Spike glycoprotein E1
B: Spike glycoprotein E1
C: Spike glycoprotein E1
D: Spike glycoprotein E1
E: Spike glycoprotein E1
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E1
J: Spike glycoprotein E2
K: Spike glycoprotein E1
L: Spike glycoprotein E2
M: Spike glycoprotein E1
N: Spike glycoprotein E2
O: Spike glycoprotein E1
P: Spike glycoprotein E2
Q: Capsid protein C
R: Capsid protein C
S: Capsid protein C
T: Capsid protein C
x 60


Theoretical massNumber of molelcules
Total (without water)15,502,9941200
Polymers15,502,9941200
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Spike glycoprotein E1
B: Spike glycoprotein E1
C: Spike glycoprotein E1
D: Spike glycoprotein E1
E: Spike glycoprotein E1
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E1
J: Spike glycoprotein E2
K: Spike glycoprotein E1
L: Spike glycoprotein E2
M: Spike glycoprotein E1
N: Spike glycoprotein E2
O: Spike glycoprotein E1
P: Spike glycoprotein E2
Q: Capsid protein C
R: Capsid protein C
S: Capsid protein C
T: Capsid protein C
x 5


  • icosahedral pentamer
  • 1.29 MDa, 100 polymers
Theoretical massNumber of molelcules
Total (without water)1,291,916100
Polymers1,291,916100
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Spike glycoprotein E1
B: Spike glycoprotein E1
C: Spike glycoprotein E1
D: Spike glycoprotein E1
E: Spike glycoprotein E1
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E1
J: Spike glycoprotein E2
K: Spike glycoprotein E1
L: Spike glycoprotein E2
M: Spike glycoprotein E1
N: Spike glycoprotein E2
O: Spike glycoprotein E1
P: Spike glycoprotein E2
Q: Capsid protein C
R: Capsid protein C
S: Capsid protein C
T: Capsid protein C
x 6


  • icosahedral 23 hexamer
  • 1.55 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)1,550,299120
Polymers1,550,299120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Spike glycoprotein E1


Mass: 31440.787 Da / Num. of mol.: 4 / Fragment: E1 ectodomain domains I+II, residues 1-290 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12 / References: UniProt: P03316
#2: Protein
Spike glycoprotein E1


Mass: 9447.606 Da / Num. of mol.: 4 / Fragment: E1 ectodomain domain III, residues 295-383 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12 / References: UniProt: P03316
#3: Protein/peptide
Spike glycoprotein E1


Mass: 3410.192 Da / Num. of mol.: 4 / Fragment: E1 transmembrane region, residues 409-439 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12 / References: UniProt: P03316
#4: Protein/peptide
Spike glycoprotein E2


Mass: 3751.593 Da / Num. of mol.: 4 / Fragment: E2 transmembrane region, residues 363-398 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12 / References: UniProt: P11259, UniProt: P03316*PLUS
#5: Protein
Capsid protein C / / coat protein C


Mass: 16545.631 Da / Num. of mol.: 4 / Fragment: Capsid protein, residues 114-264 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-IDDetails
1E2-N318Q Sindbis virusVIRUS0
2Spike glycoprotein E1, E1 ectodomain domains I+II1APPLY 60 ICOSHEDRAL SYMMETRY OPERATIONS AS MATRICES TO OBTAIN THE WHOLE COMPLEX
3Spike glycoprotein E1, E1 ectodomain domain III1APPLY 60 ICOSHEDRAL SYMMETRY OPERATIONS AS MATRICES TO OBTAIN THE WHOLE COMPLEX
4Spike glycoprotein E1, E1 transmembrane region1APPLY 60 ICOSHEDRAL SYMMETRY OPERATIONS AS MATRICES TO OBTAIN THE WHOLE COMPLEX
5Spike glycoprotein E2, E2 transmembrane region1APPLY 60 ICOSHEDRAL SYMMETRY OPERATIONS AS MATRICES TO OBTAIN THE WHOLE COMPLEX
6Capsid protein C, residues 114-2641APPLY 60 ICOSHEDRAL SYMMETRY OPERATIONS AS MATRICES TO OBTAIN THE WHOLE COMPLEX
Details of virusHost category: EUKARYOTES / Type: VIRION
Natural hostStrain: Baby Hamster Kidney
Buffer solutionName: 50 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA / pH: 7.4 / Details: 50 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: See Pletnev et al. (2001) Cell 105:127-136 for experimental details on sample preparation
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Jun 21, 2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 93.15 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM
Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON MICROSCOPY DATA.

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2EMfitmodel fitting
3PURDUE PROGRAMS3D reconstruction
CTF correctionDetails: Fourier transform of each image was modified
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: cross-common lines / Resolution: 9 Å / Num. of particles: 7085 / Actual pixel size: 1.785 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-ID
11I9W1
21WYK1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms18071 0 0 0 18071

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