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Electron microscopy of Influenza hemagglutinin (Malaysia/2506/2004) in complex with neutralizing antibody (Fab CR9114

by single particle reconstruction, at 18 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3.6, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.6, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2146
TitleElectron microscopy of Influenza hemagglutinin (Malaysia/2506/2004) in complex with neutralizing antibody (Fab CR9114
MapInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
SampleInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
KeywordsInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
AuthorsKhayat R, Lee JH, Ekiert DC, Dreyfus C, Wilson IA, Ward AB
DateDeposition: 2012-06-26, Header release: 2012-07-09, Map release: 2012-08-22, Last update: 2012-09-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3.6, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.6, Image by UCSF CHIMERA

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

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleScience, Vol. 337, Issue 6100, Page 1343-8, Year 2012
TitleHighly conserved protective epitopes on influenza B viruses.
AuthorsCyrille Dreyfus, Nick S Laursen, Ted Kwaks, David Zuijdgeest, Reza Khayat, Damian C Ekiert, Jeong Hyun Lee, Zoltan Metlagel, Miriam V Bujny, Mandy Jongeneelen, Remko van der Vlugt, Mohammed Lamrani, Hans J W M Korse, Eric Geelen, Özcan Sahin, Martijn Sieuwerts, Just P J Brakenhoff, Ronald Vogels, Olive T W Li, Leo L M Poon, Malik Peiris, Wouter Koudstaal, Andrew B Ward, Ian A Wilson, Jaap Goudsmit, Robert H E Friesen
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
KeywordsAmino Acid Sequence, Animals, Antibodies, Monoclonal (chemistry), Antibodies, Neutralizing (chemistry), Conserved Sequence, Hemagglutinin Glycoproteins, Influenza Virus (immunology), Humans, Immunodominant Epitopes (chemistry), Influenza B virus (immunology), Influenza Vaccines (immunology), Mice, Molecular Sequence Data, Neutralization Tests, Orthomyxoviridae Infections (prevention & control), Protein Conformation, hemagglutinin HA1, influenza B virus
LinksDOI: 10.1126/science.1222908, PubMed: 22878502, PMC: PMC3538841
Map
Fileemd_2146.map.gz ( map file in CCP4 format, 16001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
2.18 A/pix
= 348.8 A
160 pix
2.18 A/pix
= 348.8 A
160 pix
2.18 A/pix
= 348.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:3.6 (by author), 3.6 (movie #1):
Minimum - Maximum: -10.30411053 - 20.88138771
Average (Standard dev.): 0E-8 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
Unit CellA= B= C: 348.80002 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.18 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.182.182.18
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-10.30420.8810.000
Annotation DetailsInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
Supplement
Images
Images
Sample
NameInfluenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR9114), negative stained, single particle analysis
Number of Components2
Oligomeric StateOne trimer of hemagglutining binds to three Fabs
Theoretical Mass0.282MDa
DetailsThe sample was monodisperse
Mass-estimation MethodAmino acid sequence
Experimental Mass0.282MDa
Component #1: protein - Influenza Hemagglutinin
Scientific nameInfluenza Hemagglutinin
Theoretical Mass0.049 MDa
Experimental Mass0.049 MDa
Oligomeric DetailsTrimer
Number of Copies3
Scientific Name of SpeciesInfluenza B virus (B/Malaysia/2506/2004)
Common Name of SpeciesInfluenza
NCBI taxonomy464417
Recombinant expressionYes
Engineered SourceVector: pDCE198
Expression system: Sf9
Experiment
Sample Preparation
StainingGrids with adsorbed protein floated on 2% w/v uranyl formate for 30 seconds
Specimen Conc0.1 mg/ml
Specimen Support Details400 mesh gold grid with thin carbon support, glow discharged in amylamine atmosphere
Specimen Stateparticle
BufferDetails: 20 mM HEPES 8.0, 50mM NaCl
pH: 8
Vitrification
Cryogen NameNONE
Humidity18
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Date18-JUL-2011
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose16 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 100000, Calibrated: 100000
AstigmatismObjective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus400 nm - 1200 nm
Specimen Holder
ModelSIDE ENTRY, EUCENTRIC
Tilt Angle0 degrees - 55 degrees
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Image Acquisition
Od Range1.4
Number of Digital Images200
Sampling Size10.9
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmCommon lines with EMAN2
SoftwareEMAN2, and, Sparx
CTF CorrectionEach particle
Resolution By Author18 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections7128
DetailsParticles were selected using DoG Picker and processed using a combination of EMAN2 and Sparx.
Applied SymmetryC3 (3 fold cyclic)
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
Refinement Protocolrigid body
Refinement SpaceREAL
Target CriteriaCorrelation coefficient
SoftwareMolrep, Chimera
PDB Entry ID4FQH
Model #1
Refinement SpaceREAL
Target CriteriaCorrelation coefficient
Refinement Protocolrigid body
DetailsProtocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
SoftwareMolrep, Chimera
PDB Entry ID4FQK
Download
Data from EMDB
Header (meta data in XML format)emd-2146.xml (9.2 KB)
Map dataemd_2146.map.gz (12.1 MB)
Imagesemd_2146.png (29.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2146
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 27.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 27.3 KB