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- EMDB-1510: Structure of full-length Epac2 in complex with cyclic-AMP and Rap. -

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Basic information

Entry
Database: EMDB / ID: 1510
TitleStructure of full-length Epac2 in complex with cyclic-AMP and Rap.
KeywordsGEF / GTPases / Epac / Rap / cAMP
SampleEpac2-cAMP-Rap1B complex
SourceHomo sapiens / human
Mus musculus / mammal / House Mouse / ハツカネズミ, はつかねずみ /
Synthetic construct
Map dataThis is a map of the Epac2-cAMP-Rap1B complex.
Methodsingle particle reconstruction, at 23 Å resolution
AuthorsArias-Palomo E / Rehmann H / Hadders M / Schwede F / Bos JL / Llorca O
CitationNature, 2008, 455, 124-127

Nature, 2008, 455, 124-127 StrPapers
Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B.
Holger Rehmann / Ernesto Arias-Palomo / Michael A Hadders / Frank Schwede / Oscar Llorca / Johannes L Bos

DateDeposition: Apr 25, 2008 / Header (metadata) release: Apr 28, 2008 / Map release: Mar 31, 2009 / Last update: Apr 16, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.041906294
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.041906294
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1510.map.gz (map file in CCP4 format, 433 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
48 pix
4.2 Å/pix.
= 201.6 Å
48 pix
4.2 Å/pix.
= 201.6 Å
48 pix
4.2 Å/pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.2 Å
Density
Contour Level:0.0144 (by author), 0.0419063 (movie #1):
Minimum - Maximum-0.0394806 - 0.166338
Average (Standard dev.)0.00176734 (0.0126218)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions484848
Origin000
Limit474747
Spacing484848
CellA=B=C: 201.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.24.24.2
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z201.600201.600201.600
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS484848
D min/max/mean-0.0390.1660.002

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Supplemental data

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Sample components

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Entire Epac2-cAMP-Rap1B complex

EntireName: Epac2-cAMP-Rap1B complex / Number of components: 3
Oligomeric State: One monomer of Epac2 binds one monomer of Rap1B in presence of cAMP
MassTheoretical: 135 kDa

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Component #1: protein, Rap1B

ProteinName: Rap1B / a.k.a: Rap1B / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 18 kDa
SourceSpecies: Homo sapiens / human
External referencesGene Ontology: GO: 0005622 / InterPro: InterPro: 003577

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Component #2: protein, Epac2

ProteinName: Epac2 / a.k.a: Epac2 / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 115 kDa
SourceSpecies: Mus musculus / mammal / House Mouse / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pGEX4T
External referencesInterPro: InterPro: 001895 / Gene Ontology: GO: 0019933

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Component #3: ligand, Adenosine cyclic monophosphate

LigandName: Adenosine cyclic monophosphate / a.k.a: cAMP / Details: cAMP is the Epac2 activator. / Recombinant expression: No
MassTheoretical: 0.32921 kDa
SourceSpecies: Synthetic construct

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50mM Tris-HCL, 100mM NaCl, 10mM CaCl2, 500 uM cAMP, 5% glycerol.
pH: 7.4
Support film400 mesh Copper/Palladium grid
StainingGrids with adsorbed protein floated on 2% w/v uranyl formate for 60 seconds
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 1230 / Date: Jul 19, 2007 / Details: Microscope JEOL 1230
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Cs: 2.9 mm / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: OTHER
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: OTHER / Sampling size: 10.5 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 233 / Number of projections: 3442 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Maximum-likelihood multirefine / Software: EMAN,Xmipp / CTF correction: Phase correction at the micrograph level / Resolution: 23 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 3CF6

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