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- PDB-1ryh: Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase -

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Basic information

Entry
Database: PDB / ID: 1ryh
TitleAlternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
Componentsras-related C3 botulinum toxin substrate 1 isoform Rac1b
KeywordsHYDROLASE / GTP binding
Function / homology
Function and homology information


embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation ...embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / interneuron migration / kinocilium / regulation of hydrogen peroxide metabolic process / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / cochlea morphogenesis / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / positive regulation of skeletal muscle acetylcholine-gated channel clustering / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / cell projection assembly / positive regulation of bicellular tight junction assembly / ruffle organization / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / regulation of neuron migration / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / PCP/CE pathway / RHO GTPases activate KTN1 / Activation of RAC1 / MET activates RAP1 and RAC1 / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / Azathioprine ADME / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / positive regulation of neutrophil chemotaxis / positive regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / superoxide anion generation / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Activation of RAC1 downstream of NMDARs / dendrite morphogenesis / Rho GDP-dissociation inhibitor binding / regulation of cell size / synaptic transmission, GABAergic / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / pericentriolar material / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / regulation of postsynapse assembly / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / regulation of neuronal synaptic plasticity / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / RHO GTPases activate IQGAPs / phagocytic cup / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / actin filament polymerization
Similarity search - Function
Small GTPase Rho / Small GTPase Rho domain profile. / 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 / Rossmann fold ...Small GTPase Rho / Small GTPase Rho domain profile. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAhmadian, M.R. / Fiegen, D.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
Authors: Fiegen, D. / Haeusler, L.C. / Blumenstein, L. / Herbrand, U. / Dvorsky, R. / Vetter, I.R. / Ahmadian, M.R.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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_ref_seq_dif.details / _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: ras-related C3 botulinum toxin substrate 1 isoform Rac1b
B: ras-related C3 botulinum toxin substrate 1 isoform Rac1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8336
Polymers44,7402
Non-polymers1,0934
Water5,332296
1
A: ras-related C3 botulinum toxin substrate 1 isoform Rac1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9163
Polymers22,3701
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ras-related C3 botulinum toxin substrate 1 isoform Rac1b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9163
Polymers22,3701
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.550, 78.670, 96.880
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 1 isoform Rac1b / Rac1b


Mass: 22369.801 Da / Num. of mol.: 2 / Fragment: residues 1-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.39 Å3/Da / Density % sol: 48.05 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.5
22 mM1dropMgCl2
30.5 mMRac1b1drop
42 mMdithiothreitol1drop
5100000 nMGppNHp1drop
6100 mMHEPES1reservoirpH7.5
718-30 %PEG33501reservoir
82-6 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.75→26.261 Å / Num. obs: 40221
Reflection
*PLUS
Lowest resolution: 26.26 Å / Num. obs: 38875 / % possible obs: 96 % / Num. measured all: 138306 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.85 Å / % possible obs: 90.1 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.75

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MH1

1mh1


Resolution: 1.75→26.26 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.13 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21887 2014 5 %RANDOM
Rwork0.18081 ---
all0.18278 ---
obs0.18278 38205 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.973 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 66 296 2923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222701
X-RAY DIFFRACTIONr_bond_other_d0.0020.022477
X-RAY DIFFRACTIONr_angle_refined_deg1.8832.0043688
X-RAY DIFFRACTIONr_angle_other_deg0.96735792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6545334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1320.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022890
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02484
X-RAY DIFFRACTIONr_nbd_refined0.2230.2491
X-RAY DIFFRACTIONr_nbd_other0.2450.22729
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0060.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1521.51690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90622740
X-RAY DIFFRACTIONr_scbond_it2.81631011
X-RAY DIFFRACTIONr_scangle_it4.2944.5948
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 119
Rwork0.205 2808
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8441.0991-1.41992.5482-0.35612.2449-0.17040.38230.1943-0.13730.20290.01670.0432-0.1982-0.03250.0701-0.0271-0.03610.03890.03830.0467-5.11562.77441.168
22.6487-0.1039-0.95711.8857-0.02261.80880.0369-0.25840.20350.14880.01880.0165-0.00990.083-0.05570.0185-0.0102-0.00850.0238-0.02520.07678.17962.9697.361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2013 - 203
2X-RAY DIFFRACTION2BB1 - 1993 - 201
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.88

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