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- EMDB-1418: Binding of a neutralizing antibody to dengue virus alters the arr... -

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Basic information

Entry
Database: EMDB / ID: EMD-1418
TitleBinding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins
Map dataThis is a map of Fab 1A1D-2 complexed with Dengue virus
Sample
  • Sample: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
  • Virus: Dengue virus 2
  • Protein or peptide: Fab fragment of MAb 1A1D-2
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane
Similarity search - Function
Flavivirus envelope glycoprotein E, stem/anchor domain / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 envelope glycoprotein E, stem/anchor domain / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse) / Dengue virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsLok SM
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 7, 2007-
Header (metadata) releaseSep 7, 2007-
Map releaseJan 2, 2008-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.98
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.98
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2r6p
  • Surface level: 1.98
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2r6p
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1418.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of Fab 1A1D-2 complexed with Dengue virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.74 Å/pix.
x 288 pix.
= 789.12 Å
2.74 Å/pix.
x 288 pix.
= 789.12 Å
2.74 Å/pix.
x 288 pix.
= 789.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.74 Å
Density
Contour Level1: 1.98 / Movie #1: 1.98
Minimum - Maximum-4.12769 - 8.46468
Average (Standard dev.)0.00957931 (±0.995975)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-144-144-144
Dimensions288288288
Spacing288288288
CellA=B=C: 789.12 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.742.742.74
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z789.120789.120789.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-30-49
NX/NY/NZ6060100
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
D min/max/mean-4.1288.4650.010

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Supplemental data

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Sample components

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Entire : Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus

EntireName: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
Components
  • Sample: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
  • Virus: Dengue virus 2
  • Protein or peptide: Fab fragment of MAb 1A1D-2

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Supramolecule #1000: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus

SupramoleculeName: Fab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
type: sample / ID: 1000
Oligomeric state: The Fab molecule binds to two of the three E proteins in the icosahedral assymmetric unit
Number unique components: 2

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Supramolecule #1: Dengue virus 2

SupramoleculeName: Dengue virus 2 / type: virus / ID: 1 / Name.synonym: DENV / NCBI-ID: 11060 / Sci species name: Dengue virus 2 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: No / Syn species name: DENV
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: envelope / Diameter: 240 Å / T number (triangulation number): 3

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Macromolecule #1: Fab fragment of MAb 1A1D-2

MacromoleculeName: Fab fragment of MAb 1A1D-2 / type: protein_or_peptide / ID: 1 / Name.synonym: 1A1D-2 / Number of copies: 2 / Oligomeric state: heterodimer / Recombinant expression: No
Source (natural)Organism: Mus musculus (house mouse) / synonym: House mouse / Cell: hybridoma
Molecular weightExperimental: 50 MDa / Theoretical: 50 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.6 / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Guillotine-style plunge freezeing device
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

MicroscopeFEI/PHILIPS CM200T
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51040 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.37 µm / Nominal defocus min: 2.27 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 98 K
Alignment procedureLegacy - Astigmatism: live FFT
Detailslow dose
DateMar 21, 2007
Image recordingCategory: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 7 µm / Average electron dose: 24 e/Å2

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider,XMIPP / Number images used: 2885

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID -:

Chain - Chain ID - 1: R / Chain - Chain ID - 2: 2 / Chain - Chain ID - 3: 9
SoftwareName: EMFIT
DetailsProtocol: Rigid body
RefinementProtocol: RIGID BODY FIT
Output model

PDB-2r6p:
Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed with dengue 2 virus.

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