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- EMDB-1103: Global conformational rearrangements during the activation of the... -

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Basic information

Entry
Database: EMDB / ID: EMD-1103
TitleGlobal conformational rearrangements during the activation of the GDP/GTP exchange factor Vav3.
Map data3D reconstruction of wild type Vav3
Sample
  • Sample: wild type Vav3
  • Protein or peptide: vav3
Function / homologysmall GTPase-mediated signal transduction
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 22.0 Å
AuthorsLlorca O / Arias-Palomo E / Zugaza JL / Bustelo XR
CitationJournal: EMBO J / 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 /
Abstract: Activation of Rho/Rac GTPases during cell signaling requires the participation of GDP/GTP exchange factors of the Dbl family. Although the structure of the catalytic core of Dbl proteins has been ...Activation of Rho/Rac GTPases during cell signaling requires the participation of GDP/GTP exchange factors of the Dbl family. Although the structure of the catalytic core of Dbl proteins has been established recently, the molecular changes that the full-length proteins experience during normal or oncogenic conditions of stimulation are still unknown. Here, we have used single-particle electron microscopy to solve the structures of the inactive (unphosphorylated), active (phosphorylated), and constitutively active (N-terminally deleted) versions of the exchange factor Vav3. Comparison of these forms has revealed the interdomain interactions maintaining the inactive Vav3 state and the dynamic changes that the overall Vav3 structure undergoes upon tyrosine phosphorylation. We have also found that the conformations of phosphorylated Vav3 and N-terminally deleted Vav3 are distinct, indicating that the acquisition of constitutive activity by exchange factors is structurally more complex than the mere elimination of inhibitory interactions between structural domains.
History
DepositionJan 19, 2005-
Header (metadata) releaseJan 19, 2005-
Map releaseJan 19, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1103.gif

emd_1103.tif

Downloads & links

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Map

FileDownload / File: emd_1103.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of wild type Vav3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 80 pix.
= 323.9 Å		4.1 Å/pix.
x 80 pix.
= 323.9 Å		4.1 Å/pix.
x 80 pix.
= 323.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.607 / Movie #1: 4.4
Minimum - Maximum-4.43099 - 7.9132
Average (Standard dev.)0.0659214 (±0.541105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 323.9 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z797979
origin x/y/z0.0000.0000.000
length x/y/z323.900323.900323.900
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-4.4317.9130.066

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Supplemental data

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Sample components

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Entire : wild type Vav3

EntireName: wild type Vav3
Components
  • Sample: wild type Vav3
  • Protein or peptide: vav3

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Supramolecule #1000: wild type Vav3

SupramoleculeName: wild type Vav3 / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 98 KDa / Method: From its sequence

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Macromolecule #1: vav3

MacromoleculeName: vav3 / type: protein_or_peptide / ID: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: baculovirus-infected S. frugiperda cells / Location in cell: cytoplasm
Molecular weightExperimental: 98 KDa
Recombinant expressionOrganism: S. frugiperda
SequenceGO: small GTPase-mediated signal transduction

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 50 mM Tris-HCl, 100 mM NaCl
StainingType: NEGATIVE
Details: Glow-discharged carbon-coated grids and negatively stained with 1% w/v uranyl acetate
GridDetails: 400 mesh copper-rhodium grids
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 1230
TemperatureAverage: 293 K
Alignment procedureLegacy - Astigmatism: correction with CCD camera
DetailsElectron microscope was JEOL JEM-120, 120kV. Specimen holder, JEOL type M: 207EM-11020.
DateMar 21, 2003
Image recordingCategory: FILM / Film or detector model: KODAK 4489 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10 µm / Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.9 mm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5431

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Atomic model buiding 1

Initial model(PDB ID:

1h67

,

1f5x

,

1awe

,

1tbo

,

1gri

)
SoftwareName: SITUS
DetailsProtocol: Rigid-body. The domains were fitted computationally using the software package SITUS
RefinementProtocol: RIGID BODY FIT / Target criteria: Correlation coeficient

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