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- PDB-9rfb: Crystal Structure of Human Rac1 in Complex with the Scaffold Prot... -

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Basic information

Entry
Database: PDB / ID: 9rfb
TitleCrystal Structure of Human Rac1 in Complex with the Scaffold Protein POSH (residues 321-348)
Components
  • E3 ubiquitin-protein ligase SH3RF1
  • Ras-related C3 botulinum toxin substrate 1
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 / PHOSPHATE ION / 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: 1.854 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
B: Ras-related C3 botulinum toxin substrate 1
C: E3 ubiquitin-protein ligase SH3RF1
D: E3 ubiquitin-protein ligase SH3RF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,45811
Polymers46,1394
Non-polymers1,3187
Water7,026390
1
A: Ras-related C3 botulinum toxin substrate 1
C: E3 ubiquitin-protein ligase SH3RF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6164
Polymers23,0702
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-25 kcal/mol
Surface area9760 Å2
2
B: Ras-related C3 botulinum toxin substrate 1
D: E3 ubiquitin-protein ligase SH3RF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8417
Polymers23,0702
Non-polymers7725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-53 kcal/mol
Surface area9780 Å2
Unit cell
Length a, b, c (Å)54.793, 54.793, 329.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 20158.322 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GRR belongs to expression TAG / Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase
#2: Protein/peptide E3 ubiquitin-protein ligase SH3RF1 / Plenty of SH3s / Protein POSH / RING finger protein 142 / RING-type E3 ubiquitin transferase SH3RF1 ...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: 2911.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Peptide of POSH region 321-348 / Source: (synth.) Homo sapiens (human)
References: UniProt: Q7Z6J0, RING-type E3 ubiquitin transferase

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Non-polymers , 5 types, 397 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M phosphate, 20% (w/v) PEG 8000. RAC1 6 mg/mL , GMPPNP 1mM, POSH 3 mM

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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: Jul 22, 2022 / Details: EH1 OH2
RadiationMonochromator: Diamonds / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.854→19.67 Å / Num. obs: 34144 / % possible obs: 94.2 % / Redundancy: 13.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.052 / Rrim(I) all: 0.193 / Net I/σ(I): 8
Reflection shellResolution: 1.854→2.027 Å / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1707 / CC1/2: 0.812 / Rpim(I) all: 0.389 / Rrim(I) all: 1.2 / % possible all: 67

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
autoPROC1.0.5 (20230222)data reduction
autoPROC1.0.5 (20230222)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.854→19.67 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.468 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2263 1710 5.008 %
Rwork0.1946 32434 -
all0.196 --
obs-34144 76.982 %
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: 23.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.299 Å2-0 Å2-0 Å2
2---0.299 Å2-0 Å2
3---0.598 Å2
Refinement stepCycle: LAST / Resolution: 1.854→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3086 0 73 390 3549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123258
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163092
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6574435
X-RAY DIFFRACTIONr_angle_other_deg0.4921.5657139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.773518
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.16152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29310528
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.86510123
X-RAY DIFFRACTIONr_chiral_restr0.0780.2524
X-RAY DIFFRACTIONr_chiral_restr_other0.3250.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
X-RAY DIFFRACTIONr_nbd_refined0.2110.2565
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.22667
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21549
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21589
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0260.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.212
X-RAY DIFFRACTIONr_nbd_other0.2070.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1630.22
X-RAY DIFFRACTIONr_mcbond_it1.4631.5931603
X-RAY DIFFRACTIONr_mcbond_other1.4591.5931603
X-RAY DIFFRACTIONr_mcangle_it2.2842.8511996
X-RAY DIFFRACTIONr_mcangle_other2.2832.8531997
X-RAY DIFFRACTIONr_scbond_it2.3891.8961655
X-RAY DIFFRACTIONr_scbond_other2.3721.8921654
X-RAY DIFFRACTIONr_scangle_it3.6623.362437
X-RAY DIFFRACTIONr_scangle_other3.6613.3622438
X-RAY DIFFRACTIONr_lrange_it6.38118.4423664
X-RAY DIFFRACTIONr_lrange_other6.31517.1253556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.854-1.9010.331110.32242X-RAY DIFFRACTION17.9485
1.901-1.9530.329250.298444X-RAY DIFFRACTION15.1193
1.953-2.0090.292290.25633X-RAY DIFFRACTION22.1553
2.009-2.070.305810.241211X-RAY DIFFRACTION43.9306
2.07-2.1370.2761090.242156X-RAY DIFFRACTION79.866
2.137-2.2110.2351520.2322584X-RAY DIFFRACTION98.5591
2.211-2.2940.2721440.2762538X-RAY DIFFRACTION99.9627
2.294-2.3860.2111290.192459X-RAY DIFFRACTION100
2.386-2.4910.2221150.1792371X-RAY DIFFRACTION100
2.491-2.610.211230.1622265X-RAY DIFFRACTION100
2.61-2.7490.1981150.1632152X-RAY DIFFRACTION100
2.749-2.9120.1981070.1682044X-RAY DIFFRACTION100
2.912-3.1080.205910.1841956X-RAY DIFFRACTION100
3.108-3.350.221870.2061830X-RAY DIFFRACTION100
3.35-3.6590.283860.2021717X-RAY DIFFRACTION100
3.659-4.0730.223870.1931537X-RAY DIFFRACTION100
4.073-4.670.149650.1421403X-RAY DIFFRACTION100
4.67-5.6410.196660.1771218X-RAY DIFFRACTION100
5.641-7.6690.25520.233993X-RAY DIFFRACTION100
7.669-19.670.271360.217681X-RAY DIFFRACTION100
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)
11.6252-0.34760.23871.1748-0.24240.64760.04390.10460.04430.03-0.0655-0.00530.01320.0070.02160.0970.03840.02030.03160.01210.006119.30364.73326.4622
20.5135-0.2028-0.2430.4827-0.05531.29270.06390.0092-0.00740.0053-0.03870.0103-0.00220.0981-0.02520.10140.0457-0.01840.0661-0.00180.006741.9807-20.508915.9588
32.20950.99670.28251.6202-0.58436.2723-0.02310.04350.2335-0.0216-0.0103-0.243-0.35230.33290.03340.08540.00740.0160.03140.00450.136435.59388.945627.5339
42.05450.54321.16021.25390.36881.81730.03310.068-0.12790.15180.04470.20910.12670.1311-0.07770.15550.02030.00990.04140.010.067432.1876-26.128.5503
Refinement TLS groupSelection: ALL

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