[English] 日本語
Yorodumi
- PDB-3muw: Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3muw
TitlePseudo-atomic structure of the E2-E1 protein shell in Sindbis virus
Components(Structural polyprotein) x 2
KeywordsVIRUS / icosahedral protein shell / icosahedral 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
Function and homology information
Specimen sourceSindbis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9 Å resolution
AuthorsLi, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Nature / Year: 2010
Title: Structural changes of envelope proteins during alphavirus fusion.
Authors: Long Li / Joyce Jose / Ye Xiang / Richard J Kuhn / Michael G Rossmann
Abstract: Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens. Entry of virus into host cells by endocytosis is controlled by two envelope ...Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens. Entry of virus into host cells by endocytosis is controlled by two envelope glycoproteins, E1 and E2. The E2-E1 heterodimers form 80 trimeric spikes on the icosahedral virus surface, 60 with quasi-three-fold symmetry and 20 coincident with the icosahedral three-fold axes arranged with T = 4 quasi-symmetry. The E1 glycoprotein has a hydrophobic fusion loop at one end and is responsible for membrane fusion. The E2 protein is responsible for receptor binding and protects the fusion loop at neutral pH. The lower pH in the endosome induces the virions to undergo an irreversible conformational change in which E2 and E1 dissociate and E1 forms homotrimers, triggering fusion of the viral membrane with the endosomal membrane and then releasing the viral genome into the cytoplasm. Here we report the structure of an alphavirus spike, crystallized at low pH, representing an intermediate in the fusion process and clarifying the maturation process. The trimer of E2-E1 in the crystal structure is similar to the spikes in the neutral pH virus except that the E2 middle region is disordered, exposing the fusion loop. The amino- and carboxy-terminal domains of E2 each form immunoglobulin-like folds, consistent with the receptor attachment properties of E2.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 3, 2010 / Release: Nov 24, 2010
RevisionDateData content typeGroupProviderType
1.0Nov 24, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
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: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein


Theoretical massNumber of molelcules
Total (without water)319,2828
Polyers319,2828
Non-polymers00
Water0
1
A: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)19,156,897480
Polyers19,156,897480
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: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein
x 5


  • icosahedral pentamer
  • 1.6 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,596,40840
Polyers1,596,40840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein
x 6


  • icosahedral 23 hexamer
  • 1.92 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,915,69048
Polyers1,915,69048
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
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 envelope glycoprotein / Spike glycoprotein E2 / 6K protein / E1 envelope glycoprotein / Spike glycoprotein E1 / Coordinate model: Cα atoms only


Mass: 41311.758 Da / Num. of mol.: 4 / Source: (natural) Sindbis virus / Strain: Toto64 / References: UniProt:P03316, EC:3.4.21.- (Serine proteases)
#2: Protein/peptide
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 envelope glycoprotein / Spike glycoprotein E2 / 6K protein / E1 envelope glycoprotein / Spike glycoprotein E1 / Coordinate model: Cα atoms only


Mass: 38508.645 Da / Num. of mol.: 4 / Source: (natural) Sindbis virus / Strain: Toto64 / 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 ID
1Sindbis virusVIRUS0
2E2-E1 protein shell of Sindbis virus1
Details of virusVirus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: TNE buffer / Details: TNE buffer / pH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: This grid plus sample was kept at 100 K
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200T / 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 / Calibrated magnification: 39220 / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM

-
Processing

EM software
IDNameCategory
1EMFitmodel fitting
2PURDUE PROGRAMS3D reconstruction
CTF correctionDetails: CTF correction of each particle.
SymmetryPoint symmetry: I
3D reconstructionMethod: model-based common lines / Resolution: 9 Å / Number of particles: 7085 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf
Atomic model buildingPDB-ID: 3MUU
Number of atoms included #LASTProtein: 2468 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2468

+
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

+
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

+
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.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more