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Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins

by single particle (icosahedral) reconstruction, at 24 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.98, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.98, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2r6p, Surface level: 1.98, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-2r6p, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1418
TitleBinding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins
MapThis is a map of Fab 1A1D-2 complexed with Dengue virus
SampleFab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
AuthorsLok SM
DateDeposition: 2007-09-07, Header release: 2007-09-07, Map release: 2008-01-02, Last update: 2012-10-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.98, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.98, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2r6p, Surface level: 1.98, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-2r6p, Image by Jmol

Supplemental images
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Related Structure Data
Related Entries

PDB-2r6p

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Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 15, Issue 3, Page 312-7, Year 2008
TitleBinding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins.
AuthorsShee-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
Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907-2054, USA.
KeywordsAntibodies, Monoclonal (chemistry), Antibodies, Viral (chemistry), Binding Sites, Cryoelectron Microscopy, Crystallography, X-Ray, Dengue Virus (chemistry), Membrane Glycoproteins (chemistry), Neutralization Tests, Temperature
LinksDOI: 10.1038/nsmb.1382, PubMed: 18264114
Map
Fileemd_1418.map.gz ( map file in CCP4 format, 93313 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
2.74 A/pix
= 789.12 A
288 pix
2.74 A/pix
= 789.12 A
288 pix
2.74 A/pix
= 789.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.98, 1.98 (movie #1):
Minimum - Maximum: -4.12769 - 8.46468
Average (Standard dev.): 0.00957931 (0.995975)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin-144-144-144
Limit143143143
Spacing288288288
Unit CellA= B= C: 789.12 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.74 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-30-30-49
NX/NY/NZ6060100
MAP C/R/S123
start NC/NR/NS-144-144-144
NC/NR/NS288288288
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-4.1288.4650.010
Annotation DetailsThis is a map of Fab 1A1D-2 complexed with Dengue virus
Supplement
Images
Images
Sample
NameFab Fragment of MAb 1A1D-2 complexed with Dengue 2 virus
Oligomeric StateThe Fab molecule binds to two of the three E proteins in the icosahedral assymmetric unit
Number of Components2
Component #1: virus - DENV
Scientific nameDengue virus 2
Common NameDENV
Scientific Name of SpeciesDengue virus 2
Common Name of SpeciesDENV
NCBI taxonomy11060
EnvelopedYes
EmptyNo
ClassVIRION
IsolateSEROTYPE
Natural SourceHost Category: VERTEBRATES
NCBI taxonomy: 9606
Host Species: Homo sapiens
ShellID: 1 , Name Element: envelope , T Number: 3 , Diameter: 240 A
Component #2: protein - 1A1D-2
Scientific nameFab fragment of MAb 1A1D-2
Common Name1A1D-2
Theoretical Mass50 MDa
Experimental Mass50 MDa
Oligomeric Detailsheterodimer
Number of Copies2
Scientific Name of SpeciesMus musculus

Common Name of SpeciesHouse mouse
NCBI taxonomy10090
Recombinant expressionNo
Natural SourceCell: hybridoma
Experiment
Sample Preparation
Specimen Conc0.6 mg/ml
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
pH: 7.6
Vitrification
Cryogen NameETHANE
InstrumentHOMEMADE PLUNGER
MethodA 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.
DetailsVitrification instrument: Guillotine-style plunge freezeing device
Imaging
MicroscopeFEI/PHILIPS CM200T
Date2007-03-21
Detailslow dose
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose24 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 51040
Astigmatismlive FFT
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2270 nm - 3370 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Temperature98 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Sampling Size7
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
Algorithmprojection matching
Softwarespider,XMIPP
CTF Correctioneach particle
Resolution By Author24 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections2885
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
SoftwareEMFIT
DetailsProtocol: Rigid body
PDB Entry ID1THD
PDB Chain ID2R29
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1418.xml (9.4 KB)
Map dataemd_1418.map.gz (59.2 MB)
Images1418.gif (118.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1418
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.6 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 591.8 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 3.6 MB