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- PDB-1thd: COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5... -

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Entry
Database: PDB / ID: 1thd
TitleCOMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION
ComponentsMajor envelope protein E
KeywordsVIRUS / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE VIRUS / GLYCOPROTEIN E / CRYO-EM / Icosahedral virus
Function / homology
Function and homology information


suppression by virus of host JAK-STAT cascade via inhibition of host TYK2 activity / mRNA (guanine-N7)-methyltransferase / flavivirin / host cell mitochondrion / suppression by virus of host JAK-STAT cascade via inhibition of STAT2 activity / mRNA (guanine-N7-)-methyltransferase activity / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell endoplasmic reticulum membrane / pore formation by virus in membrane of host cell / double-stranded RNA binding ...suppression by virus of host JAK-STAT cascade via inhibition of host TYK2 activity / mRNA (guanine-N7)-methyltransferase / flavivirin / host cell mitochondrion / suppression by virus of host JAK-STAT cascade via inhibition of STAT2 activity / mRNA (guanine-N7-)-methyltransferase activity / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell endoplasmic reticulum membrane / pore formation by virus in membrane of host cell / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / protein complex oligomerization / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / ion channel activity / clathrin-dependent endocytosis of virus by host cell / host cell perinuclear region of cytoplasm / RNA helicase activity / : / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / virion attachment to host cell / RNA-dependent RNA polymerase activity / protein dimerization activity / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / serine-type endopeptidase activity / host cell nucleus / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / membrane => GO:0016020 / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS2B domain profile. / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / RNA-directed RNA polymerase, flavivirus / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3, petidase S7 / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus glycoprotein central and dimerisation domain / FtsJ-like methyltransferase / Ribosomal RNA methyltransferase, FtsJ domain / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase, C-terminal / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin E-set / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / 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: 9.5 Å
AuthorsZhang, Y. / Zhang, W. / Ogata, S. / Clements, D. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G.
Citation
Journal: 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.
#1: Journal: Nat Struct Biol / Year: 2003
Title: Visualization of membrane protein domains by cryo-electron microscopy of dengue virus.
Authors: Wei Zhang / Paul R Chipman / Jeroen Corver / Peter R Johnson / Ying Zhang / Suchetana Mukhopadhyay / Timothy S Baker / James H Strauss / Michael G Rossmann / Richard J Kuhn /
Abstract: Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The ...Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The structure of mature dengue virus particles was determined to a resolution of 9.5 A by cryo-EM and image reconstruction techniques, establishing the secondary structural disposition of the 180 envelope (E) and 180 membrane (M) proteins in the lipid envelope. The alpha-helical 'stem' regions of the E molecules, as well as part of the N-terminal section of the M proteins, are buried in the outer leaflet of the viral membrane. The 'anchor' regions of E and the M proteins each form antiparallel E-E and M-M transmembrane alpha-helices, leaving their C termini on the exterior of the viral membrane, consistent with the predicted topology of the unprocessed polyprotein. This is one of only a few determinations of the disposition of transmembrane proteins in situ and shows that the nucleocapsid core and envelope proteins do not have a direct interaction in the mature virus.
History
DepositionJun 1, 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
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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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E


Theoretical massNumber of molelcules
Total (without water)131,5903
Polymers131,5903
Non-polymers00
Water0
1
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
x 60


Theoretical massNumber of molelcules
Total (without water)7,895,412180
Polymers7,895,412180
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: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
x 5


  • icosahedral pentamer
  • 658 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)657,95115
Polymers657,95115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
x 6


  • icosahedral 23 hexamer
  • 790 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)789,54118
Polymers789,54118
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
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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


Mass: 43863.398 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: P12823

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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 VIRUS / Type: VIRUS
Buffer solutionName: 50 mM TRIS, 75 mM NACL, 1 mM EDTA / pH: 7.6 / Details: 50 mM TRIS, 75 mM NACL, 1 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationDetails: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200T / Date: Jun 27, 2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 4800 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Specimen holderTemperature: 87 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 27 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
CTF correctionDetails: EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[|CTF|+WIENER*(1-|CTF|)]
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: FOURIER-BESSEL METHOD / Resolution: 9.5 Å / Nominal pixel size: 2.8 Å
Details: THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER ...Details: THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND CHENG, 1996, J.STRUCT.BIOL. 116, 120-130) AND REFINED BY THE MODEL-BASED FOURIER TRANSFORM REFINEMENT PROCEDURE (HTTP://BOND.CS.UCF.EDU/COMPUTATIONALBIOLOGY/PROJECTS/POR/HOME.HTML).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Details: METHOD--please see citation
Atomic model buildingPDB-ID: 1TG8
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1170 0 0 0 1170

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