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- PDB-3zko: The structure of ''breathing'' dengue virus. -

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Basic information

Entry
Database: PDB / ID: 3zko
TitleThe structure of ''breathing'' dengue virus.
ComponentsENVELOPE GLYCOPROTEIN
KeywordsVIRUS / BREATHING STRUCTURE / DYNAMIC STRUCTURE
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / 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. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDENGUE VIRUS 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.7 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C
AuthorsFibriansah, G. / Ng, T.S. / Kostyuchenko, V.A. / Lee, S. / Wang, J. / Lok, S.M.
CitationJournal: J Virol / Year: 2013
Title: Structural changes in dengue virus when exposed to a temperature of 37°C.
Authors: Guntur Fibriansah / Thiam-Seng Ng / Victor A Kostyuchenko / Jaime Lee / Sumarlin Lee / Jiaqi Wang / Shee-Mei Lok /
Abstract: Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This ...Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This was confirmed by our cryo-electron microscopy images of dengue virus incubated at 37°C, where viruses change their surface from smooth to rough. Here we present the cryo-electron microscopy structures of dengue virus at 37°C. Image analysis showed four classes of particles. The three-dimensional (3D) map of one of these classes, representing half of the imaged virus population, shows that the E protein shell has expanded and there is a hole at the 3-fold vertices. Fitting E protein structures into the map suggests that all of the interdimeric and some intradimeric E protein interactions are weakened. The accessibility of some previously found cryptic epitopes on this class of particles is discussed.
History
DepositionJan 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Derived calculations
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id
Revision 1.4May 8, 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

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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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  • Simplified surface model + fitted atomic model
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Assembly

Deposited unit
A: ENVELOPE GLYCOPROTEIN
B: ENVELOPE GLYCOPROTEIN
C: ENVELOPE GLYCOPROTEIN


Theoretical massNumber of molelcules
Total (without water)163,2053
Polymers163,2053
Non-polymers00
Water00
1
A: ENVELOPE GLYCOPROTEIN
B: ENVELOPE GLYCOPROTEIN
C: ENVELOPE GLYCOPROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)9,792,316180
Polymers9,792,316180
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
  • 816 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)816,02615
Polymers816,02615
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
  • 979 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)979,23218
Polymers979,23218
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))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017)
3generate(-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5)
4generate(-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5)
5generate(0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017)
6generate(-1), (-1), (1)
7generate(-0.5, 0.809017, -0.309017), (-0.809017, -0.309017, 0.5), (0.309017, 0.5, 0.809017)
8generate(0.309017, 0.5, -0.809017), (-0.5, 0.809017, 0.309017), (0.809017, 0.309017, 0.5)
9generate(0.309017, -0.5, -0.809017), (0.5, 0.809017, -0.309017), (0.809017, -0.309017, 0.5)
10generate(-0.5, -0.809017, -0.309017), (0.809017, -0.309017, -0.5), (0.309017, -0.5, 0.809017)
11generate(1), (-1), (-1)
12generate(0.5, -0.809017, 0.309017), (-0.809017, -0.309017, 0.5), (-0.309017, -0.5, -0.809017)
13generate(-0.309017, -0.5, 0.809017), (-0.5, 0.809017, 0.309017), (-0.809017, -0.309017, -0.5)
14generate(-0.309017, 0.5, 0.809017), (0.5, 0.809017, -0.309017), (-0.809017, 0.309017, -0.5)
15generate(0.5, 0.809017, 0.309017), (0.809017, -0.309017, -0.5), (-0.309017, 0.5, -0.809017)
16generate(-1), (1), (-1)
17generate(-0.5, 0.809017, -0.309017), (0.809017, 0.309017, -0.5), (-0.309017, -0.5, -0.809017)
18generate(0.309017, 0.5, -0.809017), (0.5, -0.809017, -0.309017), (-0.809017, -0.309017, -0.5)
19generate(0.309017, -0.5, -0.809017), (-0.5, -0.809017, 0.309017), (-0.809017, 0.309017, -0.5)
20generate(-0.5, -0.809017, -0.309017), (-0.809017, 0.309017, 0.5), (-0.309017, 0.5, -0.809017)
21generate(-1), (-1), (1)
22generate(-0.809017, -0.309017, 0.5), (-0.309017, -0.5, -0.809017), (0.5, -0.809017, 0.309017)
23generate(-0.5, 0.809017, 0.309017), (-0.809017, -0.309017, -0.5), (-0.309017, -0.5, 0.809017)
24generate(0.5, 0.809017, -0.309017), (-0.809017, 0.309017, -0.5), (-0.309017, 0.5, 0.809017)
25generate(0.809017, -0.309017, -0.5), (-0.309017, 0.5, -0.809017), (0.5, 0.809017, 0.309017)
26generate(1), (-1), (-1)
27generate(0.809017, 0.309017, -0.5), (-0.309017, -0.5, -0.809017), (-0.5, 0.809017, -0.309017)
28generate(0.5, -0.809017, -0.309017), (-0.809017, -0.309017, -0.5), (0.309017, 0.5, -0.809017)
29generate(-0.5, -0.809017, 0.309017), (-0.809017, 0.309017, -0.5), (0.309017, -0.5, -0.809017)
30generate(-0.809017, 0.309017, 0.5), (-0.309017, 0.5, -0.809017), (-0.5, -0.809017, -0.309017)
31generate(1), (1), (1)
32generate(0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017)
33generate(0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017)
34generate(-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017)
35generate(-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017)
36generate(-1), (1), (-1)
37generate(-0.809017, -0.309017, 0.5), (0.309017, 0.5, 0.809017), (-0.5, 0.809017, -0.309017)
38generate(-0.5, 0.809017, 0.309017), (0.809017, 0.309017, 0.5), (0.309017, 0.5, -0.809017)
39generate(0.5, 0.809017, -0.309017), (0.809017, -0.309017, 0.5), (0.309017, -0.5, -0.809017)
40generate(0.809017, -0.309017, -0.5), (0.309017, -0.5, 0.809017), (-0.5, -0.809017, -0.309017)
41generate(1), (-1), (-1)
42generate(0.309017, 0.5, 0.809017), (-0.5, 0.809017, -0.309017), (-0.809017, -0.309017, 0.5)
43generate(0.809017, 0.309017, 0.5), (0.309017, 0.5, -0.809017), (-0.5, 0.809017, 0.309017)
44generate(0.809017, -0.309017, 0.5), (0.309017, -0.5, -0.809017), (0.5, 0.809017, -0.309017)
45generate(0.309017, -0.5, 0.809017), (-0.5, -0.809017, -0.309017), (0.809017, -0.309017, -0.5)
46generate(1), (1), (1)
47generate(0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5)
48generate(0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017)
49generate(0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017)
50generate(0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5)
51generate(-1), (-1), (1)
52generate(-0.309017, -0.5, -0.809017), (-0.5, 0.809017, -0.309017), (0.809017, 0.309017, -0.5)
53generate(-0.809017, -0.309017, -0.5), (0.309017, 0.5, -0.809017), (0.5, -0.809017, -0.309017)
54generate(-0.809017, 0.309017, -0.5), (0.309017, -0.5, -0.809017), (-0.5, -0.809017, 0.309017)
55generate(-0.309017, 0.5, -0.809017), (-0.5, -0.809017, -0.309017), (-0.809017, 0.309017, 0.5)
56generate(-1), (1), (-1)
57generate(-0.309017, -0.5, -0.809017), (0.5, -0.809017, 0.309017), (-0.809017, -0.309017, 0.5)
58generate(-0.809017, -0.309017, -0.5), (-0.309017, -0.5, 0.809017), (-0.5, 0.809017, 0.309017)
59generate(-0.809017, 0.309017, -0.5), (-0.309017, 0.5, 0.809017), (0.5, 0.809017, -0.309017)
60generate(-0.309017, 0.5, -0.809017), (0.5, 0.809017, 0.309017), (0.809017, -0.309017, -0.5)

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Components

#1: Protein ENVELOPE GLYCOPROTEIN / Coordinate model: Cα atoms only


Mass: 54401.758 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) DENGUE VIRUS 2 / Strain: NEW GUINEA C / References: UniProt: Q66394, UniProt: P12823*PLUS

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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 2 / Type: VIRUS
Buffer solutionName: 10 MM TRIS-HCL, 120 MM NACL AND 1 MM EDTA / pH: 8 / Details: 10 MM TRIS-HCL, 120 MM NACL AND 1 MM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUIDE ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 21, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 18.5 e/Å2 / Film or detector model: GENERIC GATAN
Image scansNum. digital images: 302
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2EMAN13D reconstruction
3EMAN23D reconstruction
4MPSA3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: CROSS-COMMON LINES / Resolution: 13.7 Å / Num. of particles: 5861 / Nominal pixel size: 1.9 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2296. (DEPOSITION ID: 11386).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--CORRELATION REFINEMENT PROTOCOL--CRYO-EM
Atomic model buildingPDB-ID: 1P58

1p58


Accession code: 1P58 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 13.7 Å
Refinement stepCycle: LAST / Highest resolution: 13.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 0 0 1182

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