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- PDB-3th5: Crystal structure of wild-type RAC1 -

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Basic information

Entry
Database: PDB / ID: 3th5
TitleCrystal structure of wild-type RAC1
ComponentsRas-related C3 botulinum toxin substrate 1
KeywordsSIGNALING PROTEIN / Rossmann fold / GTPASE / GTP Binding / PROTEIN 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 / regulation of hydrogen peroxide metabolic process / interneuron migration / kinocilium / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / cochlea morphogenesis / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of skeletal muscle acetylcholine-gated channel clustering / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / midbrain dopaminergic neuron differentiation / ruffle organization / epithelial cell morphogenesis / cell projection assembly / positive regulation of bicellular tight junction assembly / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / regulation of neuron migration / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / motor neuron axon guidance / regulation of nitric oxide biosynthetic process / PCP/CE pathway / Activation of RAC1 / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / positive regulation of neutrophil chemotaxis / DCC mediated attractive signaling / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / positive regulation of cell-substrate adhesion / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / dendrite morphogenesis / regulation of cell size / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / synaptic transmission, GABAergic / positive regulation of dendritic spine development / positive regulation of actin filament polymerization / Rac protein signal transduction / RHO GTPases activate PAKs / pericentriolar material / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / regulation of postsynapse assembly / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / regulation of neuronal synaptic plasticity / positive regulation of focal adhesion assembly / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phagocytic cup / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / 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: 2.3 Å
AuthorsHa, B.H. / Boggon, T.J.
CitationJournal: Nat.Genet. / Year: 2012
Title: Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma.
Authors: Krauthammer, M. / Kong, Y. / Ha, B.H. / Evans, P. / Bacchiocchi, A. / McCusker, J.P. / Cheng, E. / Davis, M.J. / Goh, G. / Choi, M. / Ariyan, S. / Narayan, D. / Dutton-Regester, K. / ...Authors: Krauthammer, M. / Kong, Y. / Ha, B.H. / Evans, P. / Bacchiocchi, A. / McCusker, J.P. / Cheng, E. / Davis, M.J. / Goh, G. / Choi, M. / Ariyan, S. / Narayan, D. / Dutton-Regester, K. / Capatana, A. / Holman, E.C. / Bosenberg, M. / Sznol, M. / Kluger, H.M. / Brash, D.E. / Stern, D.F. / Materin, M.A. / Lo, R.S. / Mane, S. / Ma, S. / Kidd, K.K. / Hayward, N.K. / Lifton, R.P. / Schlessinger, J. / Boggon, T.J. / Halaban, R.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Sep 13, 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_ncs_dom_lim / 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_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
B: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5616
Polymers45,4682
Non-polymers1,0934
Water41423
1
A: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2813
Polymers22,7341
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2813
Polymers22,7341
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.925, 97.851, 51.733
Angle α, β, γ (deg.)90.00, 96.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 2 - 177 / Label seq-ID: 29 - 204

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 22734.041 Da / Num. of mol.: 2 / Fragment: UNP residues 2-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63000
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG4000, 7% isopropanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 18366 / Num. obs: 18169 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 48.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 23.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1804 / Rsym value: 0.295 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SBD

3sbd


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 21.911 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26398 910 5.1 %RANDOM
Rwork0.22912 ---
obs0.2309 17830 98.97 %-
all-17830 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.515 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20.04 Å2
2---2.34 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 66 23 2799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222863
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1062.0083915
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0415352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48724.397116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71415482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5671515
X-RAY DIFFRACTIONr_chiral_restr0.0690.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212107
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2041.51744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38522842
X-RAY DIFFRACTIONr_scbond_it0.531119
X-RAY DIFFRACTIONr_scangle_it0.8274.51069
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1311 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.230.5
Bmedium thermal0.122
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 63 -
Rwork0.333 1259 -
obs--99.1 %
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)
18.67631.28951.75935.6796-0.0748.9141-0.2774-0.24641.6547-0.11560.18160.2893-0.933-0.23060.09580.26230.0258-0.04630.7249-0.01060.5935-2.668-6.697-2.24
24.5940.96110.30573.1818-0.33426.06910.076-0.0933-0.0102-0.22310.10270.01960.3048-0.3128-0.17870.1577-0.0107-0.02970.85820.04610.2593-4.658-21.184-3.707
39.59181.3888-2.50515.6657-0.77697.8487-0.2911-0.0883-1.6185-0.07180.3042-0.37151.34540.0227-0.01310.27660.0370.05920.8137-0.0580.65065.357-40.146-27.357
45.363-0.0391-0.12186.4646-0.83595.4203-0.10170.0620.0129-0.00930.1128-0.4189-0.11880.4167-0.01120.03850.01380.01570.8921-0.06020.2878.309-25.62-28.24
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 76
2X-RAY DIFFRACTION2A77 - 177
3X-RAY DIFFRACTION3B2 - 76
4X-RAY DIFFRACTION4B77 - 177

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