+Open data
-Basic information
Entry | Database: PDB / ID: 3rap | ||||||
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Title | The small G protein Rap2 in a non catalytic complex with GTP | ||||||
Components | PROTEIN (G protein RAP2A) | ||||||
Keywords | SIGNALING PROTEIN / G PROTEIN / RAS / GTPASE / RAP2 | ||||||
Function / homology | Function and homology information Rap protein signal transduction / microvillus assembly / regulation of synapse assembly / regulation of dendrite morphogenesis / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of JNK cascade / positive regulation of protein autophosphorylation / small monomeric GTPase / negative regulation of cell migration / G protein activity ...Rap protein signal transduction / microvillus assembly / regulation of synapse assembly / regulation of dendrite morphogenesis / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of JNK cascade / positive regulation of protein autophosphorylation / small monomeric GTPase / negative regulation of cell migration / G protein activity / synaptic membrane / protein localization to plasma membrane / Schaffer collateral - CA1 synapse / establishment of protein localization / protein localization / recycling endosome / recycling endosome membrane / GDP binding / cellular response to xenobiotic stimulus / midbody / actin cytoskeleton organization / positive regulation of protein phosphorylation / GTPase activity / GTP binding / magnesium ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Menetrey, J. / Cherfils, J. | ||||||
Citation | Journal: Proteins / Year: 1999 Title: Structure of the small G protein Rap2 in a non-catalytic complex with GTP. Authors: Menetrey, J. / Cherfils, J. #1: Journal: Embo J. / Year: 1997 Title: Crystal Structures of the Small G Protein Rap2A in Complex with its Substrate GTP, with GDP and with GTPgS Authors: Cherfils, J. / Menetrey, J. / Lebras, G. / Lebras, G. / Janoueix-Lerosey, I. / De Gunzburg, J. / Garel, J.R. / Auzat, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rap.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rap.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ra/3rap ftp://data.pdbj.org/pub/pdb/validation_reports/ra/3rap | HTTPS FTP |
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-Related structure data
Related structure data | 2rapS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18945.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P10114 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.05 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: PEG 8000 20-25% TRIS-HCL 100MM PH 8 100MM MGCL2 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9798 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→16 Å / Num. obs: 16388 / % possible obs: 97.5 % / Redundancy: 4 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 15 |
Reflection | *PLUS Num. measured all: 144323 / Rmerge(I) obs: 0.072 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RAP2A-GTP HEXAGONAL FORM (PDB 2RAP) Resolution: 2.2→16 Å / σ(F): 2
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→16 Å
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Refine LS restraints |
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