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- PDB-2rap: THE SMALL G PROTEIN RAP2A IN COMPLEX WITH GTP -

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Basic information

Entry
Database: PDB / ID: 2rap
TitleTHE SMALL G PROTEIN RAP2A IN COMPLEX WITH GTP
ComponentsRAP2A
KeywordsG PROTEIN / GTP HYDROLYSIS / RAS / RAP2A
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
Ras-related protein Rap2 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain ...Ras-related protein Rap2 / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rap-2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER MAPS / Resolution: 2.6 Å
AuthorsCherfils, J. / Menetrey, J. / Lebras, G.
CitationJournal: EMBO J. / Year: 1997
Title: Crystal structures of the small G protein Rap2A in complex with its substrate GTP, with GDP and with GTPgammaS.
Authors: Cherfils, J. / Menetrey, J. / Le Bras, G. / Janoueix-Lerosey, I. / de Gunzburg, J. / Garel, J.R. / Auzat, I.
History
DepositionMay 6, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAP2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4933
Polymers18,9461
Non-polymers5472
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.500, 64.500, 84.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein RAP2A /


Mass: 18945.562 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 166 / Mutation: 17 C-TERMINAL RESIDUES TRUNCATED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTAC32 (RAP2) AND PEMR602 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P10114
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53 %
Crystal growpH: 8
Details: 25% PEG 8000, 100MM LISO4, 100MM TRIS PH 8., pH 8.0
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %PEG80001reservoir
2100 mM1reservoirLi2SO4
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 8828 / % possible obs: 98.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.065
Reflection
*PLUS
Num. measured all: 46223

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER MAPS / Resolution: 2.6→15 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.281 -9 %
Rwork0.206 --
obs0.206 6014 98.5 %
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 32 1 13 1375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d2.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Type: x_dihedral_angle_d

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