EMDB-1104: Phosphorylated and active form of Vav3

Entry

Database / ID

EM DATA BANK (EMDB) / 1104

Sample Name / Map Annotation

Phosphorylated and active form of Vav3
3D reconstruction of phosphorylated (active) form of Vav3

Authors

Llorca O, Arias-Palomo E, Zugaza JL, Bustelo XR

Movies

Movie Page

Supplemental images

Related Entries

EMDB-1103
Cite

EMDB-1105
Cite

Cite: data citing same article

Last Update

2005-01-19

Map Release Date

2006-01-19

EMDB Sites

EMDB @EBI (EU)

EMDB @RCSB (USA)

Article

Article	EMBO J., Vol. 24, Issue 7, Page 1330-40, Year 2005
Title	Global conformational rearrangements during the activation of the GDP/GTP exchange factor Vav3.
Authors	Oscar Llorca, Ernesto Arias-Palomo, José L Zugaza, Xosé R Bustelo
Affiliation	Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.
Chemicals	Adaptor Proteins, Signal Transducing, Cell Cycle Proteins, Guanine Nucleotide Exchange Factors, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-vav, Sh2d2a protein, mouse, Vav1 protein, mouse, Vav3 protein, mouse, Tyrosine (55520-40-6), Glutathione Transferase (EC 2.5.1.18)
Keywords	Adaptor Proteins, Signal Transducing, Animals, Cell Cycle Proteins, Cells, Cultured, Chromatography, Affinity, Glutathione Transferase, Guanine Nucleotide Exchange Factors, Image Processing, Computer-Assisted, Mice, Microscopy, Electron, Models, Molecular, NIH 3T3 Cells, Phosphorylation, Protein Conformation, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-vav, Spodoptera, Tyrosine
Links	PubMed: 15775967 PubMed Central: 1142542 DOI: 10.1038/sj.emboj.7600617

Map

File

emd_1104.map ( map file in CCP4 format, 2049 KB )

Projections

Density

Contour Level (movie #1):	7.3167922
Minimum:	-4.32039
Maximum:	15.61517
Average:	0.09800
Standard dev.:	-

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	80	80	80
Origin :	-40 A	-40 A	-40 A
Limit :	39 A	39 A	39 A
Spacing :	79 A	79 A	79 A

Unit Cell

A = 80.000 A , B = 80.000 A , C = 80.000 A ,
alpha = 90.000 degrees , beta = 90.000 degrees , gamma = 90.000 degrees

Pixel Spacing

	X	Y	Z
EMDB info.	4.1	4.1	4.1
CCP4 map header	1.01266	1.01266	1.01266
EM Navigator Movie #1	4.1	4.1	4.1

CCP4 map header info

under construction!

map	MAP
mode	2
A/pix X/Y/Z	1.01265822785	1.01265822785	1.01265822785
M x/y/z	79	79	79
origin x/y/z	0.000	0.000	0.000
length x/y/z	80.000	80.000	80.000
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-32	-32	-32
NX/NY/NZ	64	64	64
MAP C/R/S	1	2	3
start NC/NR/NS	-40	-40	-40
NC/NR/NS	80	80	80
start NC,NX/NR,NY/NS,NZ	-40	-40	-40
NC,NX/NR,NY/NS,NZ	80	80	80
D min/max/mean	-4.320	15.615	0.098

Details

EMAN 0/28/2004 10:47EMAN 0/28/2004 10:47 EMAN 0/28/200410:4EMAN 0/28/2004 10:48 EMAN 0/28/200410:4EMAN 0/18/2005 18:31 EMAN 0/28/200410:47
Created byIMAGIC:MRCimage =pY-vav3.mrc 19-01-20 16:06:33 /

Annotation Details

3D reconstruction of phosphorylated (active) form of Vav3

Supplement

Sample

Name	Phosphorylated and active form of Vav3
Aggregation State	single particle
Oligomeric State	monomer
Number of Components	1
Theoretical Mass	0.098 MDa
Mass-estimation Method	from its sequence
Component #1: protein - pY-vav3
Scientific name	phosphorylated vav3
Common Name	pY-vav3
Experimental Mass	0.098 MDa
Oligomeric Details	Monomer
Mutant	Yes
Natural Source	Cell: baculovirus-infected S. frugiperda cells Cell Location: cytoplasm
Engineered Source	Exp System: baculovirus-infected S. frugiperda cells
Links	Gene Ontology: GO:0007264

Experiment

Sample Preparation
Buffer	Details: 50 mM Tris-Hcl, 100 mM NaCl Sample Conc: 0.05 mg/ml pH: 7.5
Staining	Glow-dischrged carbon-coated grids and negatively stained with 1% w/v uranyl acetate
Sample Support Details	400 mesh copper-rhodium grids
Vitrification
Cryogen Name	ETHANE
Imaging
Microscope	OTHER
Date	2003-11-14
Electron Gun
Electron Source	TUNGSTEN HAIRPIN
Accelerating Voltage	100 kV
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X,
Astigmatism	correction with CCD camera
Nominal Cs	2.9 mm
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	Eucentric ( OTHER )
Temperature	293 Kelvin
Camera
Detector	KodaK 4489 film
Image Scans
Sampling Size	10 microns
Quant Bit Number	16
Details	Digitiser used: Minolta Dimage Scan Multi Pro
Scanner	OTHER

Processing

3D Reconstruction

Algorithm

Common lines for starting model, then refined using angular refinement

Software

EMAN

Resolution By Author

22.0

Resolution Method

FSC at 0.5 cut-off

EM Data Set ( single particle )

Number of Projections

3867

Atomic Model Fitting

Model #0

Refinement Protocol

Rigid Body

Target Criteria

Correlation coeficients

Software

PDB Entry ID

Details

The domains were fitted computationally using the SITUS software

Download

Data from EMDB

Header Information

emd-1104.xml ( XML format, 6,241 byte )

Map Data

emd_1104.map.gz ( 71,619 byte )Details

Images

emd_1104.tif ( 184,106 byte )
Details

FTP site (EMDB mirror)

EMD-1104

Data from PDBj EM Navigator

movie #1

	ASF format (for windows) ( 5,654,831 byte ) MOV format (for Mac) ( 5,627,081 byte ) FLV format (for web page) ( 5,708,689 byte ) Session file for UCSF-Chimera ( 20,287 byte )

movie #2

	ASF format (for windows) ( 4,819,631 byte ) MOV format (for Mac) ( 4,859,985 byte ) FLV format (for web page) ( 5,191,001 byte ) Session file for UCSF-Chimera ( 20,350 byte )