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- PDB-9rff: Crystal Structure of Human Rac1 Fused with the Scaffold Protein P... -

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Basic information

Entry
Database: PDB / ID: 9rff
TitleCrystal Structure of Human Rac1 Fused with the Scaffold Protein POSH (residues 319-371)
ComponentsRas-related C3 botulinum toxin substrate 1,E3 ubiquitin-protein ligase SH3RF1
KeywordsHYDROLASE / GTPase GTP/GDP-Binding Nucleotide binding
Function / homology
Function and homology information


regulation of CD4-positive, alpha-beta T cell differentiation / regulation of CD8-positive, alpha-beta T cell proliferation / 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 ...regulation of CD4-positive, alpha-beta T cell differentiation / regulation of CD8-positive, alpha-beta T cell proliferation / 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 / MAP-kinase scaffold activity / 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 / response to aldosterone / 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 / RHOV GTPase cycle / 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
Similarity search - Function
E3 ubiquitin-protein ligase SH3RF1, second SH3 domain / SH3RF1/SH3RF3, fourth SH3 domain / : / Zinc finger, C3HC4 type (RING finger) / Variant SH3 domain / Small GTPase Rho / Small GTPase Rho domain profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger ...E3 ubiquitin-protein ligase SH3RF1, second SH3 domain / SH3RF1/SH3RF3, fourth SH3 domain / : / Zinc finger, C3HC4 type (RING finger) / Variant SH3 domain / Small GTPase Rho / Small GTPase Rho domain profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Zinc finger RING-type profile. / Src homology 3 domains / Zinc finger, RING-type / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 1 / E3 ubiquitin-protein ligase SH3RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.248 Å
AuthorsKjaer, L.F. / Ielasi, F.S. / Palencia, A. / Jensen, M.R.
Funding support France, European Union, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0033 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
European Union (EU)HORIZON-MSCA-2022-DN-01European Union
CitationJournal: Nat Commun / Year: 2025
Title: Hierarchical Folding-Upon-Binding of an Intrinsically Disordered Protein
Authors: Kjaer, L.F. / Ielasi, F.S. / Winbolt, T. / Delaforge, E. / Tengo, M. / Bessa, L.M. / Marino-Perez, L. / Boeri-Erba, E. / Bouvignies, G. / Palencia, A. / Jensen, M.R.
History
DepositionJun 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related C3 botulinum toxin substrate 1,E3 ubiquitin-protein ligase SH3RF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2344
Polymers25,5691
Non-polymers6653
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, RAC1-POSH elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-21 kcal/mol
Surface area10790 Å2
Unit cell
Length a, b, c (Å)39.222, 73.082, 73.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ras-related C3 botulinum toxin substrate 1,E3 ubiquitin-protein ligase SH3RF1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1 / Plenty of SH3s / ...Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1 / Plenty of SH3s / Protein POSH / RING finger protein 142 / RING-type E3 ubiquitin transferase SH3RF1 / SH3 domain-containing RING finger protein 1 / SH3 multiple domains protein 2


Mass: 25569.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GRR belongs to expression TAG,GRR belongs to expression TAG
Source: (gene. exp.) Homo sapiens (human)
Gene: RAC1, TC25, MIG5, SH3RF1, KIAA1494, POSH, POSH1, RNF142, SH3MD2
Production host: Escherichia coli (E. coli)
References: UniProt: P63000, UniProt: Q7Z6J0, small monomeric GTPase, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.12 M ethylene glycol, 0.1 M imidazole-MES pH 6.5, 37% (v/v) 2-methyl-2,4-pentanediol (MPD)-PEG 1000-PEG 3500 2 mg/mL Rac1-POSH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2022 / Details: OH1 OH2
RadiationMonochromator: Diamonds / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.248→51.75 Å / Num. obs: 50198 / % possible obs: 95 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.026 / Rrim(I) all: 0.092 / Net I/σ(I): 14.9
Reflection shellResolution: 1.248→1.337 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2510 / CC1/2: 0.576 / Rpim(I) all: 0.5 / % possible all: 56

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROC1.1.7 (20211020)data reduction
autoPROC1.1.7 (20211020)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.248→51.748 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.736 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.164 2623 5.225 %
Rwork0.1338 47575 -
all0.135 --
obs-50198 84.638 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.053 Å2
Baniso -1Baniso -2Baniso -3
1--0.208 Å20 Å2-0 Å2
2--0.297 Å20 Å2
3----0.089 Å2
Refinement stepCycle: LAST / Resolution: 1.248→51.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 41 193 1931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121816
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161738
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.8322486
X-RAY DIFFRACTIONr_angle_other_deg0.6191.7454025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.60159
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.06551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86210294
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.1211066
X-RAY DIFFRACTIONr_chiral_restr0.0990.2295
X-RAY DIFFRACTIONr_chiral_restr_other0.1730.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
X-RAY DIFFRACTIONr_nbd_refined0.2240.2340
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21586
X-RAY DIFFRACTIONr_nbtor_refined0.180.2912
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2942
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2137
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.210
X-RAY DIFFRACTIONr_nbd_other0.2380.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.220
X-RAY DIFFRACTIONr_mcbond_it5.5141.662894
X-RAY DIFFRACTIONr_mcbond_other5.4811.662894
X-RAY DIFFRACTIONr_mcangle_it8.0922.9781117
X-RAY DIFFRACTIONr_mcangle_other8.0942.9821118
X-RAY DIFFRACTIONr_scbond_it6.6191.892922
X-RAY DIFFRACTIONr_scbond_other6.6161.893923
X-RAY DIFFRACTIONr_scangle_it9.4373.3781363
X-RAY DIFFRACTIONr_scangle_other9.4343.3791364
X-RAY DIFFRACTIONr_lrange_it15.15620.2982060
X-RAY DIFFRACTIONr_lrange_other14.09418.5952000
X-RAY DIFFRACTIONr_rigid_bond_restr3.81133554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.248-1.2810.212110.2692430.26743250.9610.965.87280.262
1.281-1.3160.315470.26110080.26342430.9380.95824.86450.259
1.316-1.3540.2611250.26123850.26141030.9590.95761.17480.258
1.354-1.3960.2772030.23335210.23539680.9460.96593.85080.227
1.396-1.4410.2312080.20236670.20438750.9620.9721000.192
1.441-1.4920.2161740.1635790.16337530.970.9821000.146
1.492-1.5480.1871850.12734080.1335930.9780.9881000.11
1.548-1.6110.1521760.11233100.11434860.9860.9921000.095
1.611-1.6830.1711890.10931630.11233520.9830.9921000.091
1.683-1.7650.1571440.11130740.11432180.9760.9921000.093
1.765-1.860.161390.10529250.10730640.9840.9931000.087
1.86-1.9730.1431630.10727550.10929180.9860.9931000.093
1.973-2.1090.1571340.1125830.11227170.9860.9931000.098
2.109-2.2780.1441250.11324250.11425500.9880.9931000.102
2.278-2.4950.1511540.11822110.1223660.9860.99299.95770.109
2.495-2.7880.151400.12220060.12421460.9850.9911000.118
2.788-3.2180.1511210.1417940.14119160.9870.98899.94780.14
3.218-3.9380.159750.12715680.12916430.9870.991000.137
3.938-5.5530.164640.13712260.13912900.9850.9891000.158
5.553-51.7480.168460.27240.1987710.9860.97499.87030.23

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