[English] 日本語
Yorodumi
- PDB-1ld4: Placement of the Structural Proteins in Sindbis Virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ld4
TitlePlacement of the Structural Proteins in Sindbis Virus
Components
  • Coat protein C
  • GENERAL CONTROL PROTEIN GCN4
  • Spike glycoprotein E1
KeywordsVIRUS / sindbis virus / alphavirus structure / glycoprotein organization / nucleocapsid structure / transmembrane coiled coils / Icosahedral virus
Function / homology
Function and homology information


icosahedral viral capsid, spike / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / togavirin / Oxidative Stress Induced Senescence ...icosahedral viral capsid, spike / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / togavirin / Oxidative Stress Induced Senescence / T=4 icosahedral viral capsid / TFIID-class transcription factor complex binding / amino acid biosynthetic process / ubiquitin-like protein ligase binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / cellular response to nutrient levels / cellular response to amino acid starvation / RNA polymerase II transcription regulator complex / DNA-binding transcription activator activity, RNA polymerase II-specific / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / host cell cytoplasm / membrane fusion / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / chromatin binding / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / RNA binding / identical protein binding / nucleus / membrane
Similarity search - Function
: / Basic region leucine zipper / 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 ...: / Basic region leucine zipper / 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. / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 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
General control transcription factor GCN4 / Structural polyprotein
Similarity search - Component
Biological speciesSindbis virus
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.4 Å
AuthorsZhang, W. / Mukhopadhyay, S. / Pletnev, S.V. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: J Virol / Year: 2002
Title: Placement of the structural proteins in Sindbis virus.
Authors: Wei Zhang / Suchetana Mukhopadhyay / Sergei V Pletnev / Timothy S Baker / Richard J Kuhn / Michael G Rossmann /
Abstract: The structure of the lipid-enveloped Sindbis virus has been determined by fitting atomic resolution crystallographic structures of component proteins into an 11-A resolution cryoelectron microscopy ...The structure of the lipid-enveloped Sindbis virus has been determined by fitting atomic resolution crystallographic structures of component proteins into an 11-A resolution cryoelectron microscopy map. The virus has T=4 quasisymmetry elements that are accurately maintained between the external glycoproteins, the transmembrane helical region, and the internal nucleocapsid core. The crystal structure of the E1 glycoprotein was fitted into the cryoelectron microscopy density, in part by using the known carbohydrate positions as restraints. A difference map showed that the E2 glycoprotein was shaped similarly to E1, suggesting a possible common evolutionary origin for these two glycoproteins. The structure shows that the E2 glycoprotein would have to move away from the center of the trimeric spike in order to expose enough viral membrane surface to permit fusion with the cellular membrane during the initial stages of host infection. The well-resolved E1-E2 transmembrane regions form alpha-helical coiled coils that were consistent with T=4 symmetry. The known structure of the capsid protein was fitted into the density corresponding to the nucleocapsid, revising the structure published earlier.
History
DepositionApr 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Nov 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.length_a / _cell.length_b / _cell.length_c
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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
Remark 99Chains E-L contain alpha-carbons only. The C-terminal residues of chains M-P contain alpha-carbons only.
Remark 600HETEROGEN THE COORDINATES OF UNX 1139, 1141, 1245, 1196, 1200, 1262, 1318, 4139, 4141, 4245, 4196, ...HETEROGEN THE COORDINATES OF UNX 1139, 1141, 1245, 1196, 1200, 1262, 1318, 4139, 4141, 4245, 4196, 4200, 4262, 4318, 5139, 5141, 5245, 5196, 5200, 5262, 5318, 6139, 6141, 6245, 6196, 6200, 6262, 6318 ARE THE CENTERS OF DIFFERENCE DENSITY PEAKS THAT CORRESPOND TO THE CARBOHYDRATE MOLECULES OF THE VIRION. THE COORDINATES OF UNX 1000, 4000, 5000, AND 6000 ARE THE POINTS WHERE THE GLYCOPROTEINS E1 AND E2 ENTERS INTO MEMBRANE.

-
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
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coat protein C
B: Coat protein C
C: Coat protein C
D: Coat protein C
E: GENERAL CONTROL PROTEIN GCN4
F: GENERAL CONTROL PROTEIN GCN4
G: GENERAL CONTROL PROTEIN GCN4
H: GENERAL CONTROL PROTEIN GCN4
I: GENERAL CONTROL PROTEIN GCN4
J: GENERAL CONTROL PROTEIN GCN4
K: GENERAL CONTROL PROTEIN GCN4
L: GENERAL CONTROL PROTEIN GCN4
M: Spike glycoprotein E1
N: Spike glycoprotein E1
O: Spike glycoprotein E1
P: Spike glycoprotein E1


Theoretical massNumber of molelcules
Total (without water)361,05848
Polymers361,05816
Non-polymers032
Water00
1
A: Coat protein C
B: Coat protein C
C: Coat protein C
D: Coat protein C
E: GENERAL CONTROL PROTEIN GCN4
F: GENERAL CONTROL PROTEIN GCN4
G: GENERAL CONTROL PROTEIN GCN4
H: GENERAL CONTROL PROTEIN GCN4
I: GENERAL CONTROL PROTEIN GCN4
J: GENERAL CONTROL PROTEIN GCN4
K: GENERAL CONTROL PROTEIN GCN4
L: GENERAL CONTROL PROTEIN GCN4
M: Spike glycoprotein E1
N: Spike glycoprotein E1
O: Spike glycoprotein E1
P: Spike glycoprotein E1
x 60


Theoretical massNumber of molelcules
Total (without water)21,663,4552880
Polymers21,663,455960
Non-polymers01920
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: Coat protein C
B: Coat protein C
C: Coat protein C
D: Coat protein C
E: GENERAL CONTROL PROTEIN GCN4
F: GENERAL CONTROL PROTEIN GCN4
G: GENERAL CONTROL PROTEIN GCN4
H: GENERAL CONTROL PROTEIN GCN4
I: GENERAL CONTROL PROTEIN GCN4
J: GENERAL CONTROL PROTEIN GCN4
K: GENERAL CONTROL PROTEIN GCN4
L: GENERAL CONTROL PROTEIN GCN4
M: Spike glycoprotein E1
N: Spike glycoprotein E1
O: Spike glycoprotein E1
P: Spike glycoprotein E1
x 5


  • icosahedral pentamer
  • 1.81 MDa, 80 polymers
Theoretical massNumber of molelcules
Total (without water)1,805,288240
Polymers1,805,28880
Non-polymers0160
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein C
B: Coat protein C
C: Coat protein C
D: Coat protein C
E: GENERAL CONTROL PROTEIN GCN4
F: GENERAL CONTROL PROTEIN GCN4
G: GENERAL CONTROL PROTEIN GCN4
H: GENERAL CONTROL PROTEIN GCN4
I: GENERAL CONTROL PROTEIN GCN4
J: GENERAL CONTROL PROTEIN GCN4
K: GENERAL CONTROL PROTEIN GCN4
L: GENERAL CONTROL PROTEIN GCN4
M: Spike glycoprotein E1
N: Spike glycoprotein E1
O: Spike glycoprotein E1
P: Spike glycoprotein E1
x 6


  • icosahedral 23 hexamer
  • 2.17 MDa, 96 polymers
Theoretical massNumber of molelcules
Total (without water)2,166,345288
Polymers2,166,34596
Non-polymers0192
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: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
Coat protein C / Capsid protein C


Mass: 29410.010 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein
GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / Coordinate model: Cα atoms only


Mass: 6718.774 Da / Num. of mol.: 8 / Fragment: LEUCINE-ZIPPER (residues 225-281) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P03069
#3: Protein
Spike glycoprotein E1 / FUSION PROTEIN E1


Mass: 47416.836 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / Genus: Alphavirus / References: UniProt: P03316
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 32 / Source method: obtained synthetically
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Sindbis Virus / Type: VIRUS
Details of virusHost category: VERTEBRATES / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 50mM Tris-HCl, 200mM NaCl, 0.1mM EDTA / pH: 7.5 / Details: 50mM Tris-HCl, 200mM NaCl, 0.1mM EDTA
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Crystal grow
*PLUS
Method: cryo-electron microscopy / Details: cryo-electron microscopy

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200T / Date: Jun 15, 2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTemperature: 87 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 18.4 e/Å2 / Film or detector model: KODAK SO-163 FILM
Details: films were developed in full-strength of Kodak D19 developer for 12 minutes at 20 C

-
Processing

EM software
IDNameCategory
1EMfitmodel fitting
2EM3DR3D reconstruction
CTF correctionDetails: each viral image was CTF corrected before reconstruction, based on the following equation: F(corr)=F(obs)/[|CTF|+wiener]
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: FOURIER-BESSEL method Reference: Baker, T. S., N. H. Olson, and S. D. Fuller (1999). Adding the third dimension to virus life cycles: Three-dimensional reconstruction of icosahedral viruses ...Method: FOURIER-BESSEL method Reference: Baker, T. S., N. H. Olson, and S. D. Fuller (1999). Adding the third dimension to virus life cycles: Three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs. Micro. & Mol. Bio. Rev. 63:862-922.
Resolution: 11.4 Å / Nominal pixel size: 3.68 Å / Symmetry type: POINT
Atomic model buildingB value: 1000 / Space: REAL
Details: DETAILS--The structure of the lipid-enveloped Sindbis virus has been determined by fitting atomic resolution crystallographic structures of component proteins into an 11 resolution cryo- ...Details: DETAILS--The structure of the lipid-enveloped Sindbis virus has been determined by fitting atomic resolution crystallographic structures of component proteins into an 11 resolution cryo- electron microscopy (cryoEM) map (with significant terms to 10 resolution). The E1 glycoprotein, whose structure had been determined independently for the homologous Semliki Forest virus by X-ray crystallography (Lescar, J., Roussel,A., Wein, M.W., Navaza, J., Fuller, S.D., Wengler, G., and Rey, F.A. (2001). The fusion glycoprotein shell of Semliki Forest virus- an icosahedral assembly primed for fusogenic activation at endosomal pH. Cell 105, 137-148), was fitted into the cryoEM density, in part by using the known positions of glycoprotein sites as restraints. The well-resolved transmembrane regions form coiled coils that could be fitted with the dimeric GCN4 coiled-coil structure. The helices could be seen to extend to E1 and E2 on the outside of the membrane and to the nucleocapsid on the inside. The known structure of the capsid protein (Choi, H.K., Tong, L., Minor, W., Dumas, P., Boege, U., Rossmann, M.G., and Wengler, G. (1991). Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature 354, 37-43.) was fitted into the density corresponding to the nucleocapsid, revising an earlier published structure.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11SVB

1svb

11SVB1PDBexperimental model
21YSA

1ysa

11YSA2PDBexperimental model
31I9W

1i9w

11I9W3PDBexperimental model
RefinementHighest resolution: 11.4 Å
Refinement stepCycle: LAST / Highest resolution: 11.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15648 0 32 0 15680

+
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