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Basic information

Entry
Database: PDB / ID: 3ixy
TitleThe pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53
Components
  • E53 Fab Fragment (chain H)
  • E53 Fab Fragment (chain L)
  • Envelope protein E
  • Peptide pr
KeywordsVIRUS / Dengue Virus / DENV / immature / fusion loop / Fab / E53 / ATP-binding / Envelope protein / Helicase / Hydrolase / Membrane / Nucleotide-binding / RNA replication / Transmembrane / Virion / Capsid protein / Cleavage on pair of basic residues / Core protein / Endoplasmic reticulum / Glycoprotein / Secreted
Function / homology
Function and homology information


: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / : / viral capsid / nucleoside-triphosphate phosphatase ...: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / flavivirin / 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 / ribonucleoside triphosphate phosphatase activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B ...: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / 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 / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 23 Å
AuthorsCherrier, M.V. / Kaufmann, B. / Nybakken, G.E. / Lok, S.M. / Warren, J.T. / Nelson, C.A. / Kostyuchenko, V.A. / Holdaway, H.A. / Chipman, P.R. / Kuhn, R.J. ...Cherrier, M.V. / Kaufmann, B. / Nybakken, G.E. / Lok, S.M. / Warren, J.T. / Nelson, C.A. / Kostyuchenko, V.A. / Holdaway, H.A. / Chipman, P.R. / Kuhn, R.J. / Diamond, M.S. / Rossmann, M.G. / Fremont, D.H.
CitationJournal: EMBO J / Year: 2009
Title: Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody.
Authors: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R ...Authors: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R Chipman / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / Daved H Fremont /
Abstract: Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have ...Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have defined the structure of the flavivirus cross-reactive antibody E53 that engages the highly conserved fusion loop of the West Nile virus envelope glycoprotein. Using cryo-electron microscopy, we also determined that E53 Fab binds preferentially to spikes in noninfectious, immature flavivirions but is unable to bind significantly to mature virions, consistent with the limited solvent exposure of the epitope. We conclude that the neutralizing impact of E53 and likely similar fusion-loop-specific antibodies depends on its binding to the frequently observed immature component of flavivirus particles. Our results elucidate how fusion-loop antibodies, which comprise a significant fraction of the humoral response against flaviviruses, can function to control infection without appreciably recognizing mature virions. As these highly cross-reactive antibodies are often weakly neutralizing they also may contribute to antibody-dependent enhancement and flavi virus pathogenesis thereby complicating development of safe and effective vaccines.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 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

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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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Structure viewerMolecule:
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Assembly

Deposited unit
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Peptide pr
E: Peptide pr
F: Peptide pr
G: E53 Fab Fragment (chain H)
H: E53 Fab Fragment (chain L)
I: E53 Fab Fragment (chain H)
J: E53 Fab Fragment (chain L)


Theoretical massNumber of molelcules
Total (without water)253,93510
Polymers253,93510
Non-polymers00
Water0
1
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Peptide pr
E: Peptide pr
F: Peptide pr
G: E53 Fab Fragment (chain H)
H: E53 Fab Fragment (chain L)
I: E53 Fab Fragment (chain H)
J: E53 Fab Fragment (chain L)
x 60


Theoretical massNumber of molelcules
Total (without water)15,236,103600
Polymers15,236,103600
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 protein E
B: Envelope protein E
C: Envelope protein E
D: Peptide pr
E: Peptide pr
F: Peptide pr
G: E53 Fab Fragment (chain H)
H: E53 Fab Fragment (chain L)
I: E53 Fab Fragment (chain H)
J: E53 Fab Fragment (chain L)
x 5


  • icosahedral pentamer
  • 1.27 MDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)1,269,67550
Polymers1,269,67550
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Envelope protein E
B: Envelope protein E
C: Envelope protein E
D: Peptide pr
E: Peptide pr
F: Peptide pr
G: E53 Fab Fragment (chain H)
H: E53 Fab Fragment (chain L)
I: E53 Fab Fragment (chain H)
J: E53 Fab Fragment (chain L)
x 6


  • icosahedral 23 hexamer
  • 1.52 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,523,61060
Polymers1,523,61060
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 Envelope protein E / / Coordinate model: Cα atoms only


Mass: 43904.410 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Strain: DENV2 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: O11875, UniProt: Q9WDA6*PLUS
#2: Protein Peptide pr / prM / Peptide pr / Small envelope protein M / Matrix protein / Envelope protein E / Non-structural ...prM / Peptide pr / Small envelope protein M / Matrix protein / Envelope protein E / Non-structural protein 1 / NS1 / Coordinate model: Cα atoms only


Mass: 9261.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 / Strain: DENV2 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: P18356
#3: Antibody E53 Fab Fragment (chain H) / Coordinate model: Cα atoms only


Mass: 23630.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
#4: Antibody E53 Fab Fragment (chain L) / Coordinate model: Cα atoms only


Mass: 23588.107 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DE3

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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: Immature Dengue Virus complexed with E53 Fab / Type: VIRUS
Details: T1 icosahedron with three E monomers and two Fab per asymmetric unit
Molecular weightValue: 24.4 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.6 / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Apr 4, 2008 / Details: low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM / Electron beam tilt params: 0
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47244 X / Nominal defocus max: 2728 nm / Nominal defocus min: 1876 nm / Cs: 2 mm / Astigmatism: live FFT / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: EUCENTRIC / Temperature: 98 K / Tilt angle max: -9999 ° / Tilt angle min: -9999 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2SPIDER3D reconstruction
3Xmipp3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 23 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2741 / Actual pixel size: 2.69 Å / Magnification calibration: 47244
Details: ( Details about the particle: 400 mesh copper grid )
Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1RIGID BODY FITREALREFINEMENT PROTOCOL--Rigid Body DETAILS--Each E molecule was divided into two rigid bodies, DI-DIII and DII-pr
2RIGID BODY FITREALREFINEMENT PROTOCOL--Rigid Body DETAILS--Each E molecule was divided into two rigid bodies, DI-DIII and DII-pr
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13C6D

3c6d

13C6D1PDBexperimental model
23C5X

3c5x

23C5X2PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 0 0 2281

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