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- PDB-8s1o: Crystal structure of human Rac1-GDP-Pi -

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Basic information

Entry
Database: PDB / ID: 8s1o
TitleCrystal structure of human Rac1-GDP-Pi
ComponentsRas-related C3 botulinum toxin substrate 1
KeywordsSIGNALING PROTEIN / GTPase / GDP / Phosphate
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 / 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 / cell projection assembly / positive regulation of bicellular tight junction assembly / ruffle organization / regulation of lamellipodium assembly / thioesterase binding / regulation of neuron migration / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / 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 / Azathioprine ADME / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / positive regulation of cell-substrate adhesion / 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 / synaptic transmission, GABAergic / 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 / regulation of postsynapse assembly / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / 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 / phagocytic cup / RHO GTPases activate IQGAPs / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
Authorsferrandez, Y. / Cherfils, J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Crystal structure of human Rac1-GDP-Pi
Authors: ferrandez, Y. / 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)20,2894
Polymers19,7271
Non-polymers5623
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.320, 89.580, 108.680
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-336-

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: 19726.721 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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / Details: 100 mM SPG buffer pH 5 and 25% PEG 1500

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Data collection

DiffractionMean temperature: 292.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.27→54.34 Å / Num. obs: 9544 / % possible obs: 98.39 % / Redundancy: 6.6 % / Biso Wilson estimate: 35.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1109 / Rpim(I) all: 0.04662 / Rrim(I) all: 0.1206 / Net I/σ(I): 12.08
Reflection shellResolution: 2.27→2.351 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8576 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 6511 / CC1/2: 0.791 / Rpim(I) all: 0.3529 / Rrim(I) all: 0.929 / % possible all: 99.38

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Processing

Software
NameVersionClassification
MxCuBE1.20.1_4487data collection
PHENIX1.20.1_4487refinement
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→54.34 Å / SU ML: 0.2543 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 454 4.76 %
Rwork0.2078 9079 -
obs0.2107 9533 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.95 Å2
Refinement stepCycle: LAST / Resolution: 2.27→54.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 34 52 1454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331432
X-RAY DIFFRACTIONf_angle_d0.80821955
X-RAY DIFFRACTIONf_chiral_restr0.0498223
X-RAY DIFFRACTIONf_plane_restr0.0054244
X-RAY DIFFRACTIONf_dihedral_angle_d13.7552529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.60.28731510.23722984X-RAY DIFFRACTION98.86
2.6-3.270.28081290.24052949X-RAY DIFFRACTION96.67
3.27-54.340.2561740.18683146X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: 9.3598271299 Å / Origin y: 21.8956497664 Å / Origin z: 13.4231873897 Å
111213212223313233
T0.234936928638 Å2-0.0055474602762 Å2-0.00792385734596 Å2-0.279490772572 Å2-0.00123988421633 Å2--0.247190614676 Å2
L1.30490227336 °2-0.226698613551 °2-0.393350092566 °2-1.47256402752 °2-0.549070501277 °2--1.8293893554 °2
S-0.0627522727356 Å °0.0993873910582 Å °0.0974697499078 Å °-0.0295379235855 Å °0.0627733630931 Å °-0.0175264298616 Å °0.0448887292373 Å °-0.0681804250635 Å °-0.00963366147407 Å °
Refinement TLS groupSelection details: all

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