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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
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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
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
#1
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