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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
DescriptorSpike glycoprotein E1
Spike glycoprotein E2
Capsid protein C
KeywordsVIRUS / icosahedral enveloped virus / Icosahedral virus / Virus
Specimen sourceSindbis virus / virus / シンドビスウイルス
MethodElectron microscopy (9 Å resolution / Particle / Single particle)
AuthorsMukhopadhyay, S. / Zhang, W. / Gabler, S. / Chipman, P.R. / Strauss, E.G. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G.
CitationStructure, 2006, 14, 63-73

Structure, 2006, 14, 63-73 StrPapers
Mapping the structure and function of the E1 and E2 glycoproteins in alphaviruses.
Suchetana Mukhopadhyay / Wei Zhang / Stefan Gabler / Paul R Chipman / Ellen G Strauss / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 31, 2005 / Release: Feb 7, 2006
RevisionDateData content typeGroupProviderType
1.0Feb 7, 2006Structure modelrepositoryInitial release
1.1Apr 30, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE 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

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  • 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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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
Polyers258,38320
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
Polyers15,502,9941200
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
Polyers1,291,916100
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
Polyers1,550,299120
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

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Components

#1: Polypeptide(L)
Spike glycoprotein E1


Mass: 31440.787 Da / Num. of mol.: 4 / Fragment: E1 ectodomain domains I+II, residues 1-290
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
Spike glycoprotein E1


Mass: 9447.606 Da / Num. of mol.: 4 / Fragment: E1 ectodomain domain III, residues 295-383
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)
Spike glycoprotein E1


Mass: 3410.192 Da / Num. of mol.: 4 / Fragment: E1 transmembrane region, residues 409-439
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)
Spike glycoprotein E2


Mass: 3751.593 Da / Num. of mol.: 4 / Fragment: E2 transmembrane region, residues 363-398
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P11259

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)
Capsid protein C / coat protein C


Mass: 16545.631 Da / Num. of mol.: 4 / Fragment: Capsid protein, residues 114-264
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316, EC: 3.4.21.-

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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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 virusVirus host category: EUKARYOTES / Virus type: VIRION
Natural hostStrain: Baby Hamster Kidney
Buffer solutionName: 50 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA / Details: 50 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA / pH: 7.4
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

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

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Processing

EM software
IDNameCategory
1EMFitMODEL FITTING
2EMFitMODEL FITTING
3PURDUE PROGRAMSRECONSTRUCTION
CTF correctionDetails: Fourier transform of each image was modified
SymmetryPoint symmetry: I
3D reconstructionMethod: cross-common lines / Resolution: 9 Å / Number of particles: 7085 / Actual pixel size: 1.785 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11I9W1
21WYK1
Number of atoms included #LASTProtein: 18071 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 18071

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