EMDB-1234: West Nile virus in complex with the Fab fragment of a ...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1234
Title	West Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody.
Map	map of West Nile Virus complexed with Fab fragment of neutralizing antibody E16
Sample	West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16
Authors	Kaufmann B, Nybakken GE, Chipman PR, Zhang W, Diamond MS, Fremont DH, Kuhn RJ, Rossmann MG
Date	Deposition: 2006-06-29, Header release: 2006-06-29, Map release: 2006-09-05, Last update: 2011-05-26
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 3589.788788697, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 3589.788788697, Made by UCSF CHIMERA
Supplemental images	1234.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)	Diagram EMDB-5296 EMDB-5115 EMDB-5117 EMDB-5587 EMDB-5006 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 103, Issue 33, Page 12400-4, Year 2006
Title	West Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody.
Authors	Bärbel Kaufmann, Grant E Nybakken, Paul R Chipman, Wei Zhang, Michael S Diamond, Daved H Fremont, Richard J Kuhn, Michael G Rossmann Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.
Keywords	Animals, Antibodies, Monoclonal (chemistry), Binding Sites, Cell Line, Cricetinae, Cryoelectron Microscopy, Crystallography, X-Ray, Humans, Hydrogen-Ion Concentration, Immunoglobulin Fab Fragments (chemistry), Models, Molecular, Protein Conformation, Viral Fusion Proteins (chemistry), West Nile virus (chemistry)
Links	DOI: 10.1073/pnas.0603488103, PubMed: 16895988, PMC: PMC1567891

Map

File

EMD-1234.map ( map file in CCP4 format, 109084 KB )

Projections & Slices

Size of images:

Axes	Z (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:	6.11e+03, 3589.7887887 (movie #1):
Minimum - Maximum:	-1499.93 - 11314.1
Average (Standard dev.):	703.748 (1973.49)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis order	X	Y	Z
Dimensions	301	301	301
Origin	-150	-150	-150
Limit	150	150	150
Spacing	301	301	301

Unit Cell

A= B= C: 826.516 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 2.7459 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.7459003322259	2.7459003322259	2.7459003322259
M x/y/z	301	301	301
origin x/y/z	0.000	0.000	0.000
length x/y/z	826.516	826.516	826.516
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-64	-64	-64
NX/NY/NZ	128	128	128
MAP C/R/S	1	2	3
start NC/NR/NS	-150	-150	-150
NC/NR/NS	301	301	301
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-1499.928	11314.149	703.748

Annotation Details

map of West Nile Virus complexed with Fab fragment of neutralizing antibody E16

Supplement
Images
Images	1234.gif

Sample
Name	West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16
Oligomeric State	T1 icosahedron with three E monomers and two Fab per asymmetric unit
Number of Components	2
Component #1: virus - WNV
Scientific name	West Nile virus
Common Name	WNV
Scientific Name of Species	West Nile virus
Common Name of Species	WNV
NCBI taxonomy	11082
Enveloped	Yes
Empty	No
Class	VIRION
Isolate	STRAIN
Natural Source	Host Category: VERTEBRATES Host Species: Homo sapiens, insects
Shell	Id: 1 , Name Element: E glycoprotein , T Number: 1 , Diameter: 500 A
Component #2: protein - E16 Fab fragment
Scientific name	E16 Fab fragment
Oligomeric Details	Monomer
Number of Copies	120
Scientific Name of Species	unidentified
NCBI taxonomy	32644
Recombinant expression	Yes
Engineered Source	Expression system: mammalian cell line

Experiment
Sample Preparation
Specimen Support Details	400 mesh copper grid
Specimen State	particle
Buffer	Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA pH: 8
Vitrification
Cryogen Name	ETHANE
Instrument	HOMEMADE PLUNGER
Method	A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
Details	Vitrification instrument: Guillotine-style plunge freezeing device
Imaging
Microscope	FEI/PHILIPS CM300FEG/T
Details	low dose
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	300 kV
Electron Dose	22 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 47000, Calibrated: 47190
Astigmatism	live FFT at 200K mag
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1320 nm - 3880 nm
Specimen Holder
Holder	EUCENTRIC
Model	GATAN LIQUID NITROGEN
Tilt Angle	0 degrees - 0 degrees
Temperature	98 K
Camera
Detector	Kodak SO163
Image Acquisition
Number of Digital Images	78
Sampling Size	6.35
Quant Bit Number	16
Scanner	OTHER
Details	Nikon SuperCoolScan 9K scanned images binned 2x2

Processing
Method	single particle (icosahedral) reconstruction
3D reconstruction
Algorithm	polar fourier transform, fourier space matching and reconstruction
Software	PFTSEARCH, PO2R, P3DR
CTF Correction	Each particle
Resolution By Author	14.5 A
Resolution Method	FSC at 0.5 cut-off
Euler Angles Details	theta 69 to 90 degrees phi -31 to 31 degrees omega 0 to 360 degrees
Details	final map includes data to 12.8 Ang resolution (fsc 0.3 cut-off); magnification of final map standardized to a map calculated from dengue virus model coordinates (PDB accession no 1THD)
Single Particle
Number of Projections	3567
Details	The particles were selected interactively at the computer terminal.
Applied Symmetry	I (icosahedral)
Atomic Model Fitting
Model #0
PDB Entry ID	1THD PDB-1thd

Download

Data from EMDB

Header (meta data in XML format)

emd-1234.xml (10 KB)

Map data

emd_1234.map.gz (32.2 MB)

Images

1234.gif (12.9 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1234

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 5.3 MB Session file for UCSF-Chimera, 19.9 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3 MB .webm (WebM/VP8 format), 4.3 MB Session file for UCSF-Chimera, 19.9 KB