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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: EMD-1510
TitleStructure of full-length Epac2 in complex with cyclic-AMP and Rap.
Map dataThis is a map of the Epac2-cAMP-Rap1B complex.
Sample
  • Sample: Epac2-cAMP-Rap1B complex
  • Protein or peptide: Rap1B
  • Protein or peptide: Epac2
  • Ligand: Adenosine cyclic monophosphate
KeywordsGEF / GTPases / Epac / Rap / cAMP
Function / homology: / intracellular anatomical structure / Ras guanine-nucleotide exchange factors catalytic domain / cAMP-mediated signaling
Function and homology information
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsArias-Palomo E / Rehmann H / Hadders M / Schwede F / Bos JL / Llorca O
CitationJournal: Nature / Year: 2008
Title: Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B.
Authors: Holger Rehmann / Ernesto Arias-Palomo / Michael A Hadders / Frank Schwede / Oscar Llorca / Johannes L Bos /
Abstract: Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell ...Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain.
History
DepositionApr 25, 2008-
Header (metadata) releaseApr 28, 2008-
Map releaseMar 31, 2009-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: PDBe / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1510.gif

Downloads & links

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Map

FileDownload / File: emd_1510.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the Epac2-cAMP-Rap1B complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.2 Å/pix.
x 48 pix.
= 201.6 Å		4.2 Å/pix.
x 48 pix.
= 201.6 Å		4.2 Å/pix.
x 48 pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0144 / Movie #1: 0.0419063
Minimum - Maximum-0.0394806 - 0.166338
Average (Standard dev.)0.00176734 (±0.0126218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions484848
Spacing484848
CellA=B=C: 201.6 Å
α=β=γ: 90 °

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
Components
  • Sample: Epac2-cAMP-Rap1B complex
  • Protein or peptide: Rap1B
  • Protein or peptide: Epac2
  • Ligand: Adenosine cyclic monophosphate

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Supramolecule #1000: Epac2-cAMP-Rap1B complex

SupramoleculeName: Epac2-cAMP-Rap1B complex / type: sample / ID: 1000
Oligomeric state: One monomer of Epac2 binds one monomer of Rap1B in presence of cAMP
Number unique components: 3
Molecular weightTheoretical: 135 KDa

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Macromolecule #1: Rap1B

MacromoleculeName: Rap1B / type: protein_or_peptide / ID: 1 / Name.synonym: Rap1B / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 18 KDa
SequenceGO: intracellular anatomical structure / InterPro: INTERPRO: IPR003577

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Macromolecule #2: Epac2

MacromoleculeName: Epac2 / type: protein_or_peptide / ID: 2 / Name.synonym: Epac2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Molecular weightTheoretical: 115 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pGEX4T
SequenceGO: cAMP-mediated signaling
InterPro: Ras guanine-nucleotide exchange factors catalytic domain

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Macromolecule #3: Adenosine cyclic monophosphate

MacromoleculeName: Adenosine cyclic monophosphate / type: ligand / ID: 3 / Name.synonym: cAMP / Details: cAMP is the Epac2 activator. / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 329.21 Da

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 50mM Tris-HCL, 100mM NaCl, 10mM CaCl2, 500 uM cAMP, 5% glycerol.
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% w/v uranyl formate for 60 seconds
GridDetails: 400 mesh Copper/Palladium grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 1230
DetailsMicroscope JEOL 1230
DateJul 19, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10.5 µm / Bits/pixel: 8
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

CTF correctionDetails: Phase correction at the micrograph level
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN,Xmipp / Number images used: 3442
Final two d classificationNumber classes: 233

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Atomic model buiding 1

Initial modelPDB ID:

3cf6

RefinementSpace: REAL

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