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

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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
Specimen sourceSindbis virus / virus / シンドビスウイルス
MethodElectron microscopy (9 A resolution / Single particle / Vitreous ice (cryo EM))
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

DateDeposition: Mar 31, 2005 / Release: Feb 7, 2006 / Last modification: Feb 24, 2009
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
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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)258,38520
Polyers258,38520
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)15,503,1051200
Polyers15,503,1051200
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)1,291,925100
Polyers1,291,925100
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)1,550,310120
Polyers1,550,310120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • 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: 31441.014 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: 9447.671 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: 3410.207 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: 3751.608 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: 16545.770 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 experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: E2-N318Q Sindbis virus / Aggregation state: PARTICLE
Component

Assembly id: 1 / Details: APPLY 60 ICOSHEDRAL SYMMETRY OPERATIONS AS MATRICES TO OBTAIN THE WHOLE COMPLEX / Go id: 0005198

IDNameIpr id
1Spike glycoprotein E1, E1 ectodomain domains I+IIIPR002548
2Spike glycoprotein E1, E1 ectodomain domain IIIIPR002548
3Spike glycoprotein E1, E1 transmembrane regionIPR002548
4Spike glycoprotein E2, E2 transmembrane regionIPR000936
5Capsid protein C, residues 114-264
Details of the virus

Ictvdb id: 00.073.0.01.001 / Virus host growth cell: BHK / Virus isolate: STRAIN / Virus type: Virion

IDEntity assembly idVirus host category
11eukaryotic virus
22eukaryotic viru
33eukaryotic virus
44eukaryotic virus
Buffer solutionName: 50 mM Tris-Cl, 200 mM NaCl, 0.1 mM EDTA
Sample preparationpH: 7.4
Specimen supportDetails: See Pletnev et al. (2001) Cell 105:127-136 for experimental details on sample preparation

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1800 e/A2 / Illumination mode: flood beam low dose
Electron lensMode: bright field / 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 deg. / Tilt angle min: 0 deg.
CameraType: KODAK SO163 FILM
Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON MICROSCOPY DATA.
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: EMFIT
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: cross-common lines / Resolution: 9 A / Actual pixel size: 1.785 A/pix
CTF correction method: Fourier transform of each image was modified
Atomic model buildingSoftware name: EMFIT / Ref protocol: rigid body / Ref space: REAL
Atomic model buildingPDB-ID: 1Z8Y
Number of atoms included #LASTProtein: 18071 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 18071

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