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- PDB-2r69: Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue v... -

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Basic information

Entry
Database: PDB / ID: 2r69
TitleCrystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom resolution
Components
  • Heavy chain of 1A1D-2
  • Light chain of 1A1D-2
  • Major envelope protein E
Keywordsviral protein/Immune system / Fab-antigen complex / Capsid protein / Cleavage on pair of basic residues / Core protein / Envelope protein / Glycoprotein / Membrane / Transmembrane / Virion / viral protein-Immune system COMPLEX
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 / viral nucleocapsid ...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 / viral nucleocapsid / monoatomic ion transmembrane transport / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / 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
Immunoglobulin-like - #350 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 ...Immunoglobulin-like - #350 / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesDengue virus 2 Thailand/16681/84
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsLok, S.M. / Kostyuchenko, V.K. / Nybakken, G.E. / Holdaway, H.A. / Battisti, A.J. / Sukupolvi-petty, S. / Sedlak, D. / Fremont, D.H. / Chipman, P.R. / Roehrig, J.T. ...Lok, S.M. / Kostyuchenko, V.K. / Nybakken, G.E. / Holdaway, H.A. / Battisti, A.J. / Sukupolvi-petty, S. / Sedlak, D. / Fremont, D.H. / Chipman, P.R. / Roehrig, J.T. / Diamond, M.S. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Nat Struct Mol Biol / Year: 2008
Title: Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins.
Authors: Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / ...Authors: Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / Michael S Diamond / Richard J Kuhn / Michael G Rossmann /
Abstract: The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding ...The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus. Nevertheless, antibody could bind to the virus at 37 degrees C, suggesting that the virus is in dynamic motion making hidden epitopes briefly available. A cryo-electron microscope image reconstruction of the virus:Fab complex showed large changes in the organization of the E protein that exposed the epitopes on two of the three E molecules in each of the 60 icosahedral asymmetric units of the virus. The changes in the structure of the viral surface are presumably responsible for inhibiting attachment to cells.
History
DepositionSep 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major envelope protein E
H: Heavy chain of 1A1D-2
L: Light chain of 1A1D-2


Theoretical massNumber of molelcules
Total (without water)57,2723
Polymers57,2723
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.770, 66.888, 79.410
Angle α, β, γ (deg.)90.000, 113.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Major envelope protein E


Mass: 10932.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 2 Thailand/16681/84 / Genus: Flavivirus / Species: Dengue virus / Strain: 16681 / Gene: E protein / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18356, UniProt: P29990*PLUS
#2: Antibody Heavy chain of 1A1D-2


Mass: 22926.557 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balbc / Gene: immunoglobulin / Cell line (production host): hybridoma
#3: Antibody Light chain of 1A1D-2


Mass: 23412.869 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: balbc / Gene: immunoglobulin / Cell line (production host): hybridoma
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 12% PEG 3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 6433 / % possible obs: 68.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.118 / Χ2: 1.226 / Net I/σ(I): 8
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.219 / Num. unique all: 352 / Χ2: 1.123 / % possible all: 37.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.458 / Cor.coef. Fo:Fc: 0.31
Highest resolutionLowest resolution
Rotation4 Å30.41 Å
Translation4 Å30.41 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.363 634 8 %
Rwork0.313 --
obs-5817 73.2 %
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 19.789 Å2
Baniso -1Baniso -2Baniso -3
1-21.736 Å20 Å25.545 Å2
2---31.247 Å20 Å2
3---9.512 Å2
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 0 0 3888
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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