EMDB-2145: Electron microscopy of Influenza hemagglutinin (Malays...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 2145
Authors	Khayat R, Lee JH, Dreyfus C, Laursen NS, Wilson IA, Ward AB
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 4.8, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: 4.8, Made by UCSF CHIMERA
Supplemental images	emd_2145.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-2143 Cite EMDB-2144 Cite EMDB-2146 Cite EMDB-2147 Cite EMDB-2148 Cite EMDB-2149 Cite EMDB-2150 Cite PDB-4fqh Cite PDB-4fqi Cite PDB-4fqj Cite PDB-4fqk Cite PDB-4fql Cite PDB-4fqm Cite PDB-4fqv Cite PDB-4fqy Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-2144 EMDB-2147 EMDB-2148 EMDB-2146 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Science, Vol. 337, Issue 6100, Page 1343-8, Year 2012
Title	Highly conserved protective epitopes on influenza B viruses.
Authors	Cyrille 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.
Keywords	Amino 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
Links	DOI: 10.1126/science.1222908, PubMed: 22878502, PMC: PMC3538841

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 348.80002 A , B = 348.80002 A , C = 348.80002 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 2.18 A , Y = 2.18 A , Z = 2.18 A

CCP4 map header info

Annotation Details

Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR8071), negative stained, single particle analysis

Sample
Name	Influenza hemagglutinin (Malaysia/2506/2004), neutralizing antibody (Fab CR8071), negative stained, single particle analysis
Number of Components	2
Oligomeric State	Trimer
Theoretical Mass	0.282 MDa
Details	The sample was monodisperse
Mass-estimation Method	Sequence of components
Experimental Mass	0.282 MDa
Component #1: protein - Influenza hemagglutinin (Malaysia/2506/2004)
Scientific name	Influenza hemagglutinin (Malaysia/2506/2004)
Theoretical Mass	0.049 MDa
Experimental Mass	0.049 MDa
Oligomeric Details	Trimer
Number of Copies	3
Scientific Name of Species	Influenza B virus (B/Malaysia/2506/2004) (NCBI Taxonomy: 464417)
Common Name of Species	Influenza
Recombinant expression	Yes
Natural Source	Cell: Sf9
Engineered Source	Exp System: Sf9 Vector: pDCE198
Component #2: protein - IgG Fab (CR8071)
Scientific name	IgG Fab (CR8071)
Theoretical Mass	0.045 MDa
Experimental Mass	0.045 MDa
Oligomeric Details	3 monomers
Number of Copies	3
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes

Experiment
Sample Preparation
Staining	Grids with adsorbed protein floated on Nano-W for 30 seconds.
Specimen Conc	0.1 mg/ml
Specimen Support Details	400 mesh gold grid with thin carbon support, glow discharged
Specimen State	particle
Buffer	Details: 20 mM HEPES 8.0, 50mM NaCl pH: 8.0
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI TECNAI F20
Date	12-JAN-2012
Details	Weak beam illumination
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	120 kV
Electron Dose	16 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 100000 X, Calibrated: 100000 X
Astigmatism	Objective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	650 nm - 970 nm
Specimen Holder
Holder	( SIDE ENTRY, EUCENTRIC )
Tilt Angle	0 degrees - 55 degrees
Camera
Detector	Gatan Ultrascan 4000
Image Acquisition
Od Range	1.4
Scanner	OTHER
Number of Digital Images	200
Sampling Size	10.9 microns
Quant Bit Number	16
Details	Images were collected on a CCD

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Cross-common lines
Software	EMAN2/Sparx
CTF Correction	Each particle
Resolution By Author	19
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	7116
Details	Particles were selected using DoG Picker and processed using Sparx.
Atomic Model Fitting
Model #0
Details	Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
Refinement Protocol	rigid body
Refinement Space	REAL
Target Criteria	Correlation coefficient
Software	Molrep, Chimera
Model #1
Refinement Space	REAL
Target Criteria	Correlation coefficient
Refinement Protocol	rigid body
Details	Protocol: Rigid body. The hemagluttinin trimer was fit, then the Fabs were fit while imposing 3-fold non-cyrstallographic symmetry using Molrep.
Software	Molrep, Chimera

Data from EMDB

Header (meta data in XML format)

Map data

Images

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 4.9 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