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Three-dimensional structure of Dengue virus serotype 1 complexed with HMAb 14c10 Fab

by single particle (icosahedral) reconstruction, at 7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.5, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.5, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j05, Surface level: 2.5, Made by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-4cau, Surface level: 2.5, Made by UCSF CHIMERA

#5: Simplified surface model with fitted atomic model: PDB-3j05, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-4cau, Made by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5268
TitleThree-dimensional structure of Dengue virus serotype 1 complexed with HMAb 14c10 Fab
Mapcryo-EM reconstruction of a complex of Dengue serotype 1 with 14C10 antibodies
SampleDengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10
Keywordsvirus, dengue, serotype 1, mature virus, human antibody, neutralizing, serotype specific, Fab
AuthorsTeoh EP, Kukkaro P, Teo EW, Lim A, Tan TT, Shi PY, Yip A, Schul W, Leo S, Chan SH, Smith KGC, Ooi EE, Kemeny DM, Ng G, Ng ML, Alonso S, Fisher D, Hanson B, Lok SM, MacAry PA
DateDeposition: 2011-03-15, Header release: 2011-03-23, Map release: 2012-06-27, Last update: 2012-06-27
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.5, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 2.5, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j05, Surface level: 2.5, Made by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-4cau, Surface level: 2.5, Made by UCSF CHIMERA

#5: Simplified surface model with fitted atomic model: PDB-3j05, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-4cau, Made by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-3j05

CiteFit

PDB-4cau

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleSci Transl Med, Vol. 4, Issue 139, Page 139ra83, Year 2012
TitleThe structural basis for serotype-specific neutralization of dengue virus by a human antibody.
AuthorsEe Ping Teoh, Petra Kukkaro, En Wei Teo, Angeline P C Lim, Tze Tong Tan, Andy Yip, Wouter Schul, Myint Aung, Victor A Kostyuchenko, Yee Sin Leo, Soh Ha Chan, Kenneth G C Smith, Annie Hoi Yi Chan, Gang Zou, Eng Eong Ooi, D Michael Kemeny, Grace K Tan, Jowin K W Ng, Mah Lee Ng, Sylvie Alonso, Dale Fisher, Pei-Yong Shi, Brendon J Hanson, Shee-Mei Lok, Paul A MacAry
Department of Microbiology and Life Sciences Institute Immunology Programme, National University of Singapore, Singapore 117597, Singapore.
KeywordsAnimals, Antibodies, Neutralizing (pharmacology), Antiviral Agents (pharmacology), Cryoelectron Microscopy, Dengue (drug therapy), Dengue Virus (drug effects), Epitopes (immunology), Humans, Mice
LinksDOI: 10.1126/scitranslmed.3003888, PubMed: 22723463
Map
Fileemd_5268.map.gz ( map file in CCP4 format, 488283 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
500 pix
1.9 A/pix
= 950. A
500 pix
1.9 A/pix
= 950. A
500 pix
1.9 A/pix
= 950. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum: -12.80239964 - 18.50806618
Average (Standard dev.): 0E-8 (0.99999994)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions500500500
Origin-250-250-250
Limit249249249
Spacing500500500
Unit CellA= B= C: 950 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.9 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.91.91.9
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z950.000950.000950.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS500500500
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-12.80218.508-0.000
Annotation Detailscryo-EM reconstruction of a complex of Dengue serotype 1 with 14C10 antibodies
Supplement
Images
Images
Sample
NameDengue virus serotype 1 with Fab fragment of human monoclonal antibody 14c10
Number of Components2
Oligomeric State120 Fab molecules bind to one dengue virion
Component #1: virus - Dengue 1
Scientific nameDengue virus 1
Common NameDengue 1
Detailsstrain PVP 159
Scientific Name of SpeciesDengue virus 1
Common Name of SpeciesDengue 1
NCBI taxonomy11053
EnvelopedYes
EmptyNo
ClassVIRION
IsolateSTRAIN
Natural SourceHost Category: INVERTEBRATES
NCBI taxonomy: 7160
Host Species: Aedes albopictus
ShellID: 1 , T Number: 3 , Diameter: 240 A
Component #2: protein - Fab
Scientific nameantibody Fab fragment
Common NameFab
Experimental Mass50 MDa
Oligomeric Detailsmonomer
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell: CD22plus B cells
Cell Location: secreted
Organ Or Tissue: blood
Engineered SourceVector: pTT5
NCBI taxonomy: 9606
Expression system: Homo sapiens
Experiment
Sample Preparation
Specimen Support Detailslacey carbon copper grid
Specimen Stateparticle
BufferDetails: 120 mM NaCl, 12 mM Tris-HCl, pH 8.0, 1mM EDTA
pH: 8
Vitrification
Method1 second blotting
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeFEI TITAN KRIOS
Date27-SEP-2010
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose16 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 47000
Nominal Cs2.7 mm
Imaging ModeBRIGHT FIELD
Defocus760 nm - 4900 nm
Specimen Holder
ModelOTHER
Temperature100 K
Camera
DetectorGENERIC GATAN
Image Acquisition
Number of Digital Images341
Sampling Size15
Quant Bit Number16
Details4k x 4k Gatan CCD
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmCross-common lines
SoftwareEMAN, MPSA
CTF CorrectionEach particle
Resolution By Author7 A
Resolution MethodFSC 0.5
Single Particle
DetailsThe particles were selected manually.
Number of Projections2129
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Model #0
Target Criteriacorrelation
DetailsProtocol: rigid body. The domains were fitted separately using Fit In Map feature in Chimera
SoftwareChimera
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID3G7T
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5268.xml (9.1 KB)
Map dataemd_5268.map.gz (421.8 MB)
Imagesemd_5268_1.png (412 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5268
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 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), 3.3 MB
.webm (WebM/VP8 format), 5.8 MB
Session file for UCSF-Chimera, 26.6 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 356.1 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 482.4 KB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.9 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.4 MB