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- PDB-1ds6: CRYSTAL STRUCTURE OF A RAC-RHOGDI COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ds6
TitleCRYSTAL STRUCTURE OF A RAC-RHOGDI COMPLEX
Components
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
  • RHO GDP-DISSOCIATION INHIBITOR 2
KeywordsSIGNALING PROTEIN / BETA SANDWHICH / PROTEIN-PROTEIN COMPLEX / G-DOMAIN / IMMUNOGLOBULIN FOLD / WALKER FOLD / GTP-BINDING PROTEIN
Function / homology
Function and homology information


regulation of mast cell chemotaxis / cellular response to redox state / regulation of cell-substrate adhesion / lymphocyte aggregation / erythrocyte enucleation / Rho GDP-dissociation inhibitor activity / positive regulation of mast cell proliferation / negative regulation of trophoblast cell migration / regulation of respiratory burst / mast cell proliferation ...regulation of mast cell chemotaxis / cellular response to redox state / regulation of cell-substrate adhesion / lymphocyte aggregation / erythrocyte enucleation / Rho GDP-dissociation inhibitor activity / positive regulation of mast cell proliferation / negative regulation of trophoblast cell migration / regulation of respiratory burst / mast cell proliferation / regulation of neutrophil migration / regulation of mast cell degranulation / regulation of hydrogen peroxide metabolic process / NADPH oxidase complex / engulfment of apoptotic cell / respiratory burst / cortical cytoskeleton organization / regulation of Rho protein signal transduction / ROS and RNS production in phagocytes / protein kinase regulator activity / cell projection assembly / PCP/CE pathway / positive regulation of neutrophil chemotaxis / motor neuron axon guidance / positive regulation of protein targeting to mitochondrion / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / regulation of T cell proliferation / CDC42 GTPase cycle / RHOH GTPase cycle / Rho protein signal transduction / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate NADPH Oxidases / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of lamellipodium assembly / bone resorption / regulation of cell migration / GPVI-mediated activation cascade / RAC1 GTPase cycle / GTPase activator activity / regulation of actin cytoskeleton organization / actin filament organization / small GTPase binding / phagocytic vesicle membrane / Constitutive Signaling by Aberrant PI3K in Cancer / chemotaxis / lamellipodium / PIP3 activates AKT signaling / nuclear envelope / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / mitochondrial outer membrane / cytoskeleton / G protein-coupled receptor signaling pathway / focal adhesion / GTPase activity / endoplasmic reticulum membrane / GTP binding / protein kinase binding / signal transduction / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / small GTPase Rho 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 ...Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / small GTPase Rho 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 / Distorted Sandwich / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 2 / Rho GDP-dissociation inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsScheffzek, K. / Stephan, I. / Jensen, O.N. / Illenberger, D. / Gierschik, P.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The Rac-RhoGDI complex and the structural basis for the regulation of Rho proteins by RhoGDI.
Authors: Scheffzek, K. / Stephan, I. / Jensen, O.N. / Illenberger, D. / Gierschik, P.
History
DepositionJan 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2
B: RHO GDP-DISSOCIATION INHIBITOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4294
Polymers41,9612
Non-polymers4682
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.026, 61.922, 141.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 2 / P21-RAC2


Mass: 21453.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: LEUKOCYTE / Cellular location: CYTOPLASM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P15153
#2: Protein RHO GDP-DISSOCIATION INHIBITOR 2 / RHO GDI 2 / RHO-GDI BETA / LY-GDI


Mass: 20507.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: LEUKOCYTE / Cellular location: CYTOPLASM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P52566
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 3350, Lithium sulfate, Magnesium Chloride, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
220-25 %PEG33501reservoir
3100 mMMES1reservoir
4200 mM1reservoirLi2SO4
540 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.78
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 66315 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.65
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 3.37 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.91 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 98 % / Num. unique obs: 4068

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→30 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: STANDARD PROTOCOLS IN CNS, MLF- TARGET
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1815 9.7 %RANDOM
Rwork0.234 ---
obs0.234 18654 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 29 129 2997
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.852.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 299 10 %
Rwork0.274 2682 -
obs--90.7 %
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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