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- PDB-4f38: Crystal structure of geranylgeranylated RhoA in complex with RhoG... -

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Basic information

Entry
Database: PDB / ID: 4f38
TitleCrystal structure of geranylgeranylated RhoA in complex with RhoGDI in its active GPPNHP-bound form
Components
  • Rho GDP-dissociation inhibitor 1
  • Transforming protein RhoA
KeywordsCELL CYCLE/CHAPERONE / RhoA / RhoGDI / active GPPNHP bound form / CELL CYCLE-CHAPERONE complex
Function / homology
Function and homology information


RHO GTPases Activate ROCKs / SLIT2:ROBO1 increases RHOA activity / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / RHO GTPases Activate Rhotekin and Rhophilins / Axonal growth stimulation / PCP/CE pathway / RHO GTPases activate PKNs / RHO GTPases activate KTN1 / Axonal growth inhibition (RHOA activation) ...RHO GTPases Activate ROCKs / SLIT2:ROBO1 increases RHOA activity / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / RHO GTPases Activate Rhotekin and Rhophilins / Axonal growth stimulation / PCP/CE pathway / RHO GTPases activate PKNs / RHO GTPases activate KTN1 / Axonal growth inhibition (RHOA activation) / PI3K/AKT activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHOH GTPase cycle / EPHA-mediated growth cone collapse / ERBB2 Regulates Cell Motility / Rho GDP-dissociation inhibitor activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / RHOC GTPase cycle / RAC2 GTPase cycle / CDC42 GTPase cycle / G beta:gamma signalling through PI3Kgamma / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RHO GTPases activate CIT / Ovarian tumor domain proteases / RAC1 GTPase cycle / G alpha (12/13) signalling events / RHO GTPases Activate Formins / RHOA GTPase cycle / RHOG GTPase cycle / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / regulation of Rho protein signal transduction / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell size / VEGFA-VEGFR2 Pathway / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / regulation of synaptic vesicle cycle / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / motor neuron apoptotic process / odontogenesis / ossification involved in bone maturation / negative chemotaxis / apical junction complex / myosin binding / regulation of neuron projection development / stress fiber assembly / positive regulation of cytokinesis / negative regulation of vascular associated smooth muscle cell migration / negative regulation of vascular associated smooth muscle cell proliferation / cerebral cortex cell migration / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / immunological synapse / mitotic spindle assembly / negative regulation of cell-substrate adhesion / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / endothelial cell migration / positive regulation of T cell migration / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / cytoplasmic microtubule organization / cytoskeleton organization / Neutrophil degranulation / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / GTPase activator activity / regulation of cell migration / small monomeric GTPase / cell-matrix adhesion / kidney development / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization
Similarity search - Function
Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / small GTPase Rho family 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 / Distorted Sandwich / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GERAN-8-YL GERAN / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rho GDP-dissociation inhibitor 1 / Transforming protein RhoA
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGuo, Z. / Tnimov, Z. / Alexandrov, K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Quantitative Analysis of Prenylated RhoA Interaction with Its Chaperone, RhoGDI.
Authors: Tnimov, Z. / Guo, Z. / Gambin, Y. / Nguyen, U.T. / Wu, Y.W. / Abankwa, D. / Stigter, A. / Collins, B.M. / Waldmann, H. / Goody, R.S. / Alexandrov, K.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Nov 8, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA
B: Rho GDP-dissociation inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2196
Polymers45,3742
Non-polymers8454
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-30 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.000, 71.576, 136.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Transforming protein RhoA


Mass: 21994.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rhoa, Arha, Arha2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9QUI0*PLUS
#2: Protein Rho GDP-dissociation inhibitor 1 / Rho GDI 1 / GDI-1 / Rho-GDI alpha


Mass: 23379.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgdia, C87222, Gdi1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q99PT1*PLUS

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Non-polymers , 4 types, 84 molecules

#3: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSEQUENCE REFERENCES FOR THIS PROTEIN DO NOT CURRENTLY EXIST IN UNIPROT

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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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 20% (w/v) PEG 3350, 0.2M MgCl2, 0.1M Hepes-NaOH, 25mM Hepes-NaOH pH 7.2, 40mM NaCl, 3mM MgCl2, 10M GMPPNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→68.01 Å / Num. all: 21383 / Num. obs: 20741 / % possible obs: 97 % / Observed criterion σ(F): 6.9 / Observed criterion σ(I): 12.33 / Redundancy: 2.7 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.07 / Net I/σ(I): 12.33
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2156 / Rsym value: 0.279 / % possible all: 98.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOA

1doa


Resolution: 2.8→68.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.867 / SU B: 34.184 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 3.6 / σ(I): 3.6 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28133 544 4.7 %RANDOM
Rwork0.202 ---
all0.206 21383 --
obs0.20579 20741 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.387 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2---1.86 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.8→68.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 54 80 3126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223107
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.9934206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7045379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07924.485136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.04515545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5551520
X-RAY DIFFRACTIONr_chiral_restr0.1170.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212326
X-RAY DIFFRACTIONr_mcbond_it0.7161.51907
X-RAY DIFFRACTIONr_mcangle_it1.41523075
X-RAY DIFFRACTIONr_scbond_it2.09531200
X-RAY DIFFRACTIONr_scangle_it3.6964.51131
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 29 -
Rwork0.207 829 -
obs--99.65 %
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)
10.34540.0723-0.11590.887-0.09410.2274-0.00660.0274-0.02010.0805-0.058-0.06290.00230.020.06460.04740.0008-0.0149-0.00120.0040.0151-13.8612-11.486530.0296
20.36390.6647-0.0911.3793-0.17330.4273-0.01410.03850.02790.0270.04750.0229-0.00020.0177-0.03340.01380.0137-0.00580.0150.00890.0209-11.837610.727910.7324
30000000000000000.0327000.032700.0327-25.357-7.12231.233
417.5425-1.40915.7993-0.7628-3.7842-11.9345-0.6157-0.3698-0.1921-1.79470.4884-0.35340.8379-0.5390.12730.5182-0.11590.12330.0433-0.07750.0069-20.1945-21.824529.4688
50.0025-0.0075-0.0597-0.03640.00960.01120.04920.0183-0.0130.0054-0.01680.0332-0.02320.0075-0.03240.06320.018-0.00290.013-0.01650.0766-14.2991.442219.8765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 190
2X-RAY DIFFRACTION2B7 - 204
3X-RAY DIFFRACTION3A202 - 203
4X-RAY DIFFRACTION4A204
5X-RAY DIFFRACTION5A301 - 335

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