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- PDB-8s1n: Crystal structure of human Rac1-GDP -

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Basic information

Entry
Database: PDB / ID: 8s1n
TitleCrystal structure of human Rac1-GDP
ComponentsRas-related C3 botulinum toxin substrate 1
KeywordsSIGNALING PROTEIN / GTPase / GDP
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 / epithelial cell morphogenesis / ruffle organization / positive regulation of bicellular tight junction assembly / cell projection assembly / 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 / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / RHO GTPases activate KTN1 / Activation of RAC1 / MET activates RAP1 and RAC1 / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / positive regulation of cell-substrate adhesion / Azathioprine ADME / 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 / 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 / positive regulation of Rho protein signal transduction / positive regulation of dendritic spine development / establishment or maintenance of cell polarity / synaptic transmission, GABAergic / Rac protein signal transduction / positive regulation of actin filament polymerization / pericentriolar material / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / regulation of postsynapse assembly / EPH-ephrin mediated repulsion of cells / ficolin-1-rich granule membrane / anatomical structure morphogenesis / regulation of neuronal synaptic plasticity / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases / 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 / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFerrandez, Y. / Nawrotek, A. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Structure of GDP form of Rac1
Authors: Ferrandez, Y. / Nawrotek, A. / Cherfils, J.
History
DepositionFeb 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1783
Polymers19,7111
Non-polymers4682
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-18 kcal/mol
Surface area8890 Å2
Unit cell
Length a, b, c (Å)41.489, 90.340, 107.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

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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: 19710.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63000, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES 7.0, 200 mM Calcium chloride, 20% PEG 6000

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.999872 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999872 Å / Relative weight: 1
ReflectionResolution: 1.8→37.7 Å / Num. obs: 12342 / % possible obs: 64.55 % / Redundancy: 1.8 % / Biso Wilson estimate: 25.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.17
Reflection shellResolution: 1.8→1.866 Å / Num. unique obs: 28 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.20.1_4487data processing
MxCuBEdata collection
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.7 Å / SU ML: 0.2506 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2575 647 5.25 %
Rwork0.2044 11686 -
obs0.207 12333 64.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.34 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 29 102 1467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861394
X-RAY DIFFRACTIONf_angle_d1.21041902
X-RAY DIFFRACTIONf_chiral_restr0.075222
X-RAY DIFFRACTIONf_plane_restr0.0086235
X-RAY DIFFRACTIONf_dihedral_angle_d17.2706513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.2481140.3209189X-RAY DIFFRACTION5.42
1.94-2.140.30421130.27341810X-RAY DIFFRACTION51.04
2.14-2.440.2831510.23532815X-RAY DIFFRACTION78.24
2.44-3.080.26882010.22933412X-RAY DIFFRACTION94.71
3.08-37.70.23461680.17413460X-RAY DIFFRACTION91.25

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