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- PDB-2yew: Modeling Barmah Forest virus structural proteins -

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Basic information

Entry
Database: PDB / ID: 2yew
TitleModeling Barmah Forest virus structural proteins
Components
  • CAPSID PROTEIN
  • E1 ENVELOPE GLYCOPROTEIN
  • E2 ENVELOPE GLYCOPROTEIN
KeywordsVIRUS / ALPHAVIRUS / MOLECULAR DYNAMICS
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / 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 speciesBARMAH FOREST VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5 Å
AuthorsKostyuchenko, V.A. / Jakana, J. / Liu, X. / Haddow, A.D. / Aung, M. / Weaver, S.C. / Chiu, W. / Lok, S.M.
CitationJournal: J Virol / Year: 2011
Title: The structure of barmah forest virus as revealed by cryo-electron microscopy at a 6-angstrom resolution has detailed transmembrane protein architecture and interactions.
Authors: Victor A Kostyuchenko / Joanita Jakana / Xiangan Liu / Andrew D Haddow / Myint Aung / Scott C Weaver / Wah Chiu / Shee-Mei Lok /
Abstract: Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, ...Barmah Forest virus (BFV) is a mosquito-borne alphavirus that infects humans. A 6-Å-resolution cryo-electron microscopy three-dimensional structure of BFV exhibits a typical alphavirus organization, with RNA-containing nucleocapsid surrounded by a bilipid membrane anchored with the surface proteins E1 and E2. The map allows details of the transmembrane regions of E1 and E2 to be seen. The C-terminal end of the E2 transmembrane helix binds to the capsid protein. Following the E2 transmembrane helix, a short α-helical endodomain lies on the inner surface of the lipid envelope. The E2 endodomain interacts with E1 transmembrane helix from a neighboring E1-E2 trimeric spike, thereby acting as a spacer and a linker between spikes. In agreement with previous mutagenesis studies, the endodomain plays an important role in recruiting other E1-E2 spikes to the budding site during virus assembly. The E2 endodomain may thus serve as a target for antiviral drug design.
History
DepositionMar 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4Oct 23, 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

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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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
  • EMDB-1886
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  • Superimposition on EM map
  • EMDB-1886
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN
B: E1 ENVELOPE GLYCOPROTEIN
C: E2 ENVELOPE GLYCOPROTEIN
D: CAPSID PROTEIN
E: E1 ENVELOPE GLYCOPROTEIN
F: E2 ENVELOPE GLYCOPROTEIN
G: CAPSID PROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN
J: CAPSID PROTEIN
K: E1 ENVELOPE GLYCOPROTEIN
L: E2 ENVELOPE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)483,12012
Polymers483,12012
Non-polymers00
Water00
1
A: CAPSID PROTEIN
B: E1 ENVELOPE GLYCOPROTEIN
C: E2 ENVELOPE GLYCOPROTEIN
D: CAPSID PROTEIN
E: E1 ENVELOPE GLYCOPROTEIN
F: E2 ENVELOPE GLYCOPROTEIN
G: CAPSID PROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN
J: CAPSID PROTEIN
K: E1 ENVELOPE GLYCOPROTEIN
L: E2 ENVELOPE GLYCOPROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)28,987,200720
Polymers28,987,200720
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: CAPSID PROTEIN
B: E1 ENVELOPE GLYCOPROTEIN
C: E2 ENVELOPE GLYCOPROTEIN
D: CAPSID PROTEIN
E: E1 ENVELOPE GLYCOPROTEIN
F: E2 ENVELOPE GLYCOPROTEIN
G: CAPSID PROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN
J: CAPSID PROTEIN
K: E1 ENVELOPE GLYCOPROTEIN
L: E2 ENVELOPE GLYCOPROTEIN
x 5


  • icosahedral pentamer
  • 2.42 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,415,60060
Polymers2,415,60060
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: CAPSID PROTEIN
B: E1 ENVELOPE GLYCOPROTEIN
C: E2 ENVELOPE GLYCOPROTEIN
D: CAPSID PROTEIN
E: E1 ENVELOPE GLYCOPROTEIN
F: E2 ENVELOPE GLYCOPROTEIN
G: CAPSID PROTEIN
H: E1 ENVELOPE GLYCOPROTEIN
I: E2 ENVELOPE GLYCOPROTEIN
J: CAPSID PROTEIN
K: E1 ENVELOPE GLYCOPROTEIN
L: E2 ENVELOPE GLYCOPROTEIN
x 6


  • icosahedral 23 hexamer
  • 2.9 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,898,72072
Polymers2,898,72072
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))

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Components

#1: Protein
CAPSID PROTEIN / COAT PROTEIN


Mass: 28311.041 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BARMAH FOREST VIRUS / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P89946, togavirin
#2: Protein
E1 ENVELOPE GLYCOPROTEIN / SPIKE GLYCOPROTEIN E1


Mass: 46283.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BARMAH FOREST VIRUS / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P89946
#3: Protein
E2 ENVELOPE GLYCOPROTEIN / SPIKE GLYCOPROTEIN E2


Mass: 46185.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BARMAH FOREST VIRUS / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: P89946
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: BARMAH FOREST VIRUS / Type: VIRUS
Buffer solutionpH: 7.4 / Details: 0.05M Tris-HCl, pH 7.4, 0.1M NaCl, 0.001M EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC / Date: Jan 10, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 4.1 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC GATAN
Image scansNum. digital images: 760
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2EMAN3D reconstruction
3MPSA3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES, MULTIPATH SIMULTANEOUS ANNEALING PROTOCOL
Resolution: 5 Å / Num. of particles: 5169 / Nominal pixel size: 1.42 Å / Actual pixel size: 1.42 Å
Details: THE MODELS WERE BUILD USING MODELLER FOR HOMOLOGY -BASED MODELLING AND USING VMD WITH NAMD FOR FLEXIBLE FITTING INTO CRYO-EM DENSITY. CHAIN A DOES NOT CONTAIN RNA-BINDING PART, ABOUT 80 N- ...Details: THE MODELS WERE BUILD USING MODELLER FOR HOMOLOGY -BASED MODELLING AND USING VMD WITH NAMD FOR FLEXIBLE FITTING INTO CRYO-EM DENSITY. CHAIN A DOES NOT CONTAIN RNA-BINDING PART, ABOUT 80 N-TERMINAL RESIDUES. THE STRUCTURE WAS MODELED BASED ON HOMOLOGY TO PROTEIN WITH KNOWN STURUCTURE AND CRYO-EM DENSITY FITTING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- 1886. (DEPOSITION ID: 7893).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11SVP

1svp

11SVP1PDBexperimental model
22XFB

2xfb

12XFB2PDBexperimental model
32ALA

2ala

12ALA3PDBexperimental model
RefinementHighest resolution: 5 Å
Refinement stepCycle: LAST / Highest resolution: 5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31120 0 0 0 31120

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