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- PDB-1tge: The structure of immature Dengue virus at 12.5 angstrom -

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Basic information

Entry
Database: PDB / ID: 1tge
TitleThe structure of immature Dengue virus at 12.5 angstrom
Componentsenvelope glycoprotein
KeywordsVIRUS / flavivirus / dengue immature virus / prM particle / Icosahedral virus
Function / homology
Function and homology information


flavivirin / serine-type peptidase activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA helicase ...flavivirin / serine-type peptidase activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / RNA helicase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / fusion of virus membrane with host endosome membrane / : / viral envelope / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane
Similarity search - Function
Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain ...Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDengue virus 2 Puerto Rico/PR159-S1/1969
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsZhang, Y. / Zhang, W. / Ogata, S. / Clements, D. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Structure / Year: 2004
Title: Conformational changes of the flavivirus E glycoprotein.
Authors: Ying Zhang / Wei Zhang / Steven Ogata / David Clements / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann /
Abstract: Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal ...Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal fragment of E has been determined and compared with a previously described structure. The primary difference between these structures is a 10 degrees rotation about a hinge relating the fusion domain DII to domains DI and DIII. These two rigid body components were used for independent fitting of E into the cryo-electron microscopy maps of both immature and mature dengue viruses. The fitted E structures in these two particles showed a difference of 27 degrees between the two components. Comparison of the E structure in its postfusion state with that in the immature and mature virions shows a rotation approximately around the same hinge. Flexibility of E is apparently a functional requirement for assembly and infection of flaviviruses.
History
DepositionMay 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 1.4Feb 14, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Remark 999SEQUENCE AUTHORS SUBMITTED COORDINATES FOR CA ATOMS ONLY.

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Superimposition on EM map
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Assembly

Deposited unit
A: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)131,6293
Polymers131,6293
Non-polymers00
Water00
1
A: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein
x 60


Theoretical massNumber of molelcules
Total (without water)7,897,759180
Polymers7,897,759180
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: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein
x 5


  • icosahedral pentamer
  • 658 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)658,14715
Polymers658,14715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: envelope glycoprotein
B: envelope glycoprotein
C: envelope glycoprotein
x 6


  • icosahedral 23 hexamer
  • 790 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)789,77618
Polymers789,77618
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: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein envelope glycoprotein / E glycoprotein / Coordinate model: Cα atoms only


Mass: 43876.441 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dengue virus 2 Puerto Rico/PR159-S1/1969 / Genus: Flavivirus / Species: Dengue virus / Strain: PR159/S1 / References: UniProt: P27914

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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: Dengue-2 immature particle / Type: VIRUS
Details: The samples were produced by adding ammonium chloride to the media in the late infection stage
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T
Electron gunElectron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 33000 X / Nominal defocus max: 3640 nm / Nominal defocus min: 1662 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategoryDetails
1EMfitmodel fitting
2POR3D reconstructionJi et al 2003
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: See primary citation / Resolution: 12.5 Å / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--see primary citation
Atomic model buildingPDB-ID: 1TG8

1tg8


Accession code: 1TG8 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 0 0 1170

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