3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-2139

EM map of an influenza H3 hemagglutatin in complex with C05 Fab

by single particle reconstruction, at 17 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.4, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.4, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2139
AuthorsKhayat R, Lee JH, Ekiert DC, Wilson IA, Ward AB
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.4, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.4, Made by UCSF CHIMERA

Supplemental images

emd_2139.png
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-2138
Cite

EMDB-2140
Cite

PDB-4fnk
Cite

PDB-4fnl
Cite

PDB-4fp8
Cite

PDB-4fqr
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-2138

EMDB-2140

EMDB-2304
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleNature, Vol. 489, Issue 7417, Page 526-32, Year 2012
TitleCross-neutralization of influenza A viruses mediated by a single antibody loop.
AuthorsDamian C Ekiert, Arun K Kashyap, John Steel, Adam Rubrum, Gira Bhabha, Reza Khayat, Jeong Hyun Lee, Michael A Dillon, Ryann E O'Neil, Aleksandr M Faynboym, Michael Horowitz, Lawrence Horowitz, Andrew B Ward, Peter Palese, Richard Webby, Richard A Lerner, Ramesh R Bhatt, Ian A Wilson
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
KeywordsAnimals, Antibodies, Neutralizing (chemistry), Antibodies, Viral (chemistry), Antibody Specificity (genetics), Antigens, Viral (chemistry), Binding Sites, Complementarity Determining Regions (chemistry), Conserved Sequence, Cross Reactions (genetics), Crystallography, X-Ray, Enzyme-Linked Immunosorbent Assay, Epitopes (chemistry), Hemagglutinin Glycoproteins, Influenza Virus (chemistry), Influenza A Virus, H1N1 Subtype (chemistry), Influenza A Virus, H3N2 Subtype (chemistry), Influenza A virus (chemistry), Influenza Vaccines (immunology), Mice, Models, Molecular, Molecular Sequence Data, Mutation (genetics), Orthomyxoviridae Infections (immunology), Protein Conformation
LinksDOI: 10.1038/nature11414, PubMed: 22982990, PMC: PMC3538848
Map
FileEMD-2139.map ( map file in CCP4 format, 4002 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:1.4 (by author), 1.4 (movie #1):
Minimum - Maximum: -1.44750535 - 8.02569771
Average (Standard dev.): 0E-8 (1.00000000)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 100 100 100
Origin : -50 -50 -50
Limit : 49 49 49
Spacing : 100 100 100
Unit CellA = 218.0 A , B = 218.0 A , C = 218.0 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees
Pixel SpacingX = 2.18 A , Y = 2.18 A , Z = 2.18 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.182.182.18
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z218.000218.000218.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.4488.026-0.000
Annotation DetailsNegative stain reconstruction of flu HA3 in complex with C5 fab
Supplement
Images
Images

emd_2139.png
Sample
NameInfluenza HA3 in complex with C5 Fab
Number of Components2
Oligomeric StateOne HA trimer binds to 3 fabs
Component #1: protein - HA3
Scientific nameInfluenza A/Perth/16/2009 hemagglutinin
Common NameHA3
Oligomeric DetailsTrimer
Number of Copies3
Scientific Name of SpeciesInfluenza A virus (NCBI Taxonomy: 11320)
Common Name of SpeciesFlu
StrainA/Perth/16/2009
Recombinant expressionYes
Engineered SourceExp System: unidentified baculovirus (NCBI Taxonomy: 10469)
Vector: pDCE198
Component #2: protein - C05 antibody fab fragment
Scientific nameC05 antibody fab fragment
Oligomeric DetailsMonomer
Number of Copies3
Scientific Name of SpeciesHomo sapiens (NCBI Taxonomy: 9606)
Common Name of SpeciesHuman
Recombinant expressionYes
Engineered SourceVector: pFastBacDual
Exp System: unidentified baculovirus (NCBI Taxonomy: 10469)
Experiment
Sample Preparation
StainingNano-W for 30 seconds
Specimen Conc0.1 mg/ml
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 20mM HEPES pH 7.5, 50mM NaCl
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Date14-FEB-2012
DetailsImages taken from 0 to 55 degrees in 5 degree tilt increments
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose16 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 100000 X,
AstigmatismObjective lens astigmatism corrected at 100,000x
Imaging ModeBRIGHT FIELD
Defocus700 nm - 900 nm
Specimen Holder
Holder ( SIDE ENTRY, EUCENTRIC )
Tilt Angle0 degrees - 55 degrees
Temperature ( 293 Kelvin - 293 Kelvin )
Camera
DetectorGatan 4k x 4k
Image Acquisition
Number of Digital Images269
Sampling Size0.109 microns
Quant Bit Number16
DetailsImages recorded using CCD
Processing
Methodsingle particle reconstruction
3 D reconstruction
SoftwareSparx
CTF CorrectionMicrograph and each particle
Resolution By Author17
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections28766
DetailsParticles were selected using an automated particle picking program.
Download
Data from EMDB
Header (meta data in XML format)emd-2139.xml (8.2 KB)
Map dataemd_2139.map.gz (3.5 MB)
Imagesemd_2139.png (104.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2139
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 27.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 27.3 KB