[English] 日本語
Yorodumi
- PDB-1z8y: Mapping the E2 Glycoprotein of Alphaviruses -

+
Open data


ID or keywords:

Loading...

no data

-
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 / Virus
Function / homologyFlavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set ...Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / icosahedral viral capsid, spike / Togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / membrane fusion / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / host cell cytoplasm / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / Structural polyprotein / Structural polyprotein
Function and homology information
Specimen sourceSindbis virus / / virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9 Å resolution
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.
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 ...SEQUENCE Author states that it appears even though the correct sequence utilizes a lysine, leucine was used in the model.

-
Structure visualization

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

Downloads & links

-
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

-
Components

#1: Protein/peptide
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 / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12 / References: UniProt:P03316
#2: Protein/peptide
Spike glycoprotein E1


Mass: 9447.606 Da / Num. of mol.: 4 / Fragment: E1 ectodomain domain III, residues 295-383 / Source: (natural) Sindbis virus / / 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: (natural) Sindbis virus / / 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: (natural) Sindbis virus / / virus / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12 / References: UniProt:P11259, UniProt:P03316*PLUS
#5: Protein/peptide
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 / Genus: Alphavirus / Cell: Baby Hamster Kidney / Strain: TE12 / References: UniProt:P03316, EC:3.4.21.- (Serine proteases)

-
Experimental details

-
Experiment

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

-
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

-
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 FIELDBright-field microscopy / 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

-
Processing

EM software
IDNameCategory
1EMFitmodel fitting
2EMFitmodel fitting
3PURDUE PROGRAMS3D reconstruction
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more