[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...

-
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 / 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 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...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 / 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
Similarity search - Component
Biological speciesSindbis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å
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.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 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
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
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
Polymers319,2828
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
Polymers19,156,897480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Polymers1,596,40840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers1,915,69048
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


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

-
Components

#1: Protein
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 ...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 method: isolated from a natural source / Source: (natural) Sindbis virus / Strain: Toto64
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 ...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 method: isolated from a natural source / Source: (natural) Sindbis virus / Strain: Toto64
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent-ID
1Sindbis virusVIRUS0
2E2-E1 protein shell of Sindbis virus1
Details of virusHost category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: TNE buffer / pH: 7.5 / Details: TNE buffer
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

MicroscopyModel: 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 X / Calibrated magnification: 39220 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTilt angle max: 0 ° / Tilt angle min: 0 °
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 (icosahedral)
3D reconstructionMethod: model-based common lines / Resolution: 9 Å / Num. of particles: 7085 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: sumf / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 3MUU

3muu


Accession code: 3MUU / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 0 0 2468

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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