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- PDB-2r29: Neutralization of dengue virus by a serotype cross-reactive antib... -

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Basic information

Entry
Database: PDB / ID: 2r29
TitleNeutralization of dengue virus by a serotype cross-reactive antibody elucidated by cryoelectron microscopy and x-ray crystallography
Components
  • Envelope protein E
  • Heavy chain of Fab 1A1D-2
  • Light chain of Fab 1A1D-2
KeywordsViral protein/Immune system / Fab-antigen complex / ATP-binding / Capsid protein / Cleavage on pair of basic residues / Endoplasmic reticulum / Envelope protein / Glycoprotein / Helicase / Hydrolase / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Nucleotidyltransferase / Nucleus / Phosphorylation / Protease / Ribonucleoprotein / RNA replication / RNA-binding / RNA-directed RNA polymerase / Secreted / Serine protease / Transcription / Transcription regulation / Transferase / Transmembrane / Viral nucleoprotein / Virion / Viral protein-Immune system COMPLEX
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / 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 / 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 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / 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 / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / : / : / 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 ...Immunoglobulin-like - #350 / : / : / 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / 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 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
DepositionAug 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,9713
Polymers57,9713
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.120, 58.660, 78.190
Angle α, β, γ (deg.)90.000, 114.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Envelope protein E /


Mass: 10932.665 Da / Num. of mol.: 1 / Fragment: residues 478-574
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: P14340, UniProt: P29991*PLUS
#2: Antibody Heavy chain of Fab 1A1D-2


Mass: 23068.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Mouse B-Cell, Hybridoma / Source: (natural) Mus musculus (house mouse)
#3: Antibody Light chain of Fab 1A1D-2


Mass: 23969.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Mouse B-Cell, Hybridoma / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 5.4
Details: 11-13% PEG 2000, pH 5.4, 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: Oct 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 15759 / % possible obs: 90.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.123 / Χ2: 1.363 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.91.70.476770.98239.2
2.9-3.022.30.35912530.9973.1
3.02-3.152.80.31115531.0790.1
3.15-3.323.30.23917051.10898.3
3.32-3.533.70.217361.26100
3.53-3.83.80.15717461.446100
3.8-4.183.80.1317521.605100
4.18-4.793.80.10717431.563100
4.79-6.033.80.1117791.569100
6.03-503.70.0818151.263100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.49 / Cor.coef. Fo:Fc: 0.291
Highest resolutionLowest resolution
Rotation4 Å46.9 Å
Translation4 Å46.9 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / FOM work R set: 0.782
RfactorNum. reflection
Rfree0.321 1087
Rwork0.259 -
obs-10561
Displacement parametersBiso mean: 38.667 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 0 254 4234

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