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- PDB-5fr2: Farnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetyl... -

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Basic information

Entry
Database: PDB / ID: 5fr2
TitleFarnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetylated at K178
Components
  • RHO GDP-DISSOCIATION INHIBITOR 1
  • TRANSFORMING PROTEIN RHOA
KeywordsSIGNALING PROTEIN / LYSINE-ACETYLATION / RHOA / RAS-SUPERFAMILY / RHOGDI / CYTOSKELETON / GDP
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / 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 ...Rho GDP-dissociation inhibitor activity / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / 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 / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / 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 / apical junction assembly / cell 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 / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / motor neuron apoptotic process / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / EPHA-mediated growth cone collapse / myosin binding / regulation of neuron projection development / stress fiber assembly / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / ficolin-1-rich granule membrane / immunological synapse / RHOA GTPase cycle / 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 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / cytoplasmic microtubule organization / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / GTPase activator activity / regulation of cell migration / secretory granule membrane / small monomeric GTPase / cell-matrix adhesion / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell morphogenesis / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway / ruffle membrane / neuron migration
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
beta-D-glucopyranose / FARNESYL / GUANOSINE-5'-DIPHOSPHATE / Rho GDP-dissociation inhibitor 1 / Transforming protein RhoA
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsKuhlmann, N. / Wroblowski, S. / Knyphausen, P. / de Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Krueger, M. ...Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / de Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Krueger, M. / Schacherl, M. / Baumann, U. / James, L.C. / Chin, J.W. / Lammers, M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural and Mechanistic Insights Into the Regulation of the Fundamental Rho-Regulator Rhogdi Alpha by Lysine Acetylation.
Authors: Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / De Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Kruger, M. / Schacherl, M. / Baumann, U. / ...Authors: Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / De Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Kruger, M. / Schacherl, M. / Baumann, U. / James, L.C. / Chin, J.W. / Lammers, M.
History
DepositionDec 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)47,4616
Polymers46,6072
Non-polymers8544
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-33.3 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.979, 176.979, 63.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein TRANSFORMING PROTEIN RHOA / RHO CDNA CLONE 12 / H12 / RHOA


Mass: 21943.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIOESTER BETWEEN CYS190 AND FARNESYL-MOIETY / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#2: Protein RHO GDP-DISSOCIATION INHIBITOR 1 / RHO GDI 1 / RHO-GDI ALPHA / RHOGDI-ALPHA


Mass: 24663.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LYSINE-ACETYLATED AT K178 / Source: (gene. exp.) BOS TAURUS (domestic cattle) / Plasmid: PCDF-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19803

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Sugars , 1 types, 1 molecules

#6: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 20 molecules

#3: Chemical ChemComp-FAR / FARNESYL


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.28 % / Description: NONE
Crystal growDetails: 0.2 M LITHIUMSULFATE 0.1 M BIS-TRIS PH5.5 25% PEG3350 30% DEXTROSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014 / Details: MIRRORS
RadiationMonochromator: BARTELS SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→44.24 Å / Num. obs: 17709 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Biso Wilson estimate: 46.52 Å2 / Rmerge(I) obs: 0.52 / Net I/σ(I): 7.1
Reflection shellResolution: 3.35→3.62 Å / Redundancy: 15.7 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DOA

1doa


Resolution: 3.35→44.245 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 838 5 %
Rwork0.2362 --
obs0.2374 16696 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.17 Å2
Refinement stepCycle: LAST / Resolution: 3.35→44.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 56 17 2989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033027
X-RAY DIFFRACTIONf_angle_d0.7864086
X-RAY DIFFRACTIONf_dihedral_angle_d16.031162
X-RAY DIFFRACTIONf_chiral_restr0.027451
X-RAY DIFFRACTIONf_plane_restr0.003520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3508-3.56070.28671390.2692585X-RAY DIFFRACTION99
3.5607-3.83550.29371480.25322611X-RAY DIFFRACTION100
3.8355-4.22130.23911170.22332626X-RAY DIFFRACTION100
4.2213-4.83170.2311290.21362641X-RAY DIFFRACTION100
4.8317-6.08560.25641510.23042646X-RAY DIFFRACTION100
6.0856-49.07120.29291510.25842706X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 67.9201 Å / Origin y: -55.5152 Å / Origin z: -19.6459 Å
111213212223313233
T0.1926 Å20.0061 Å2-0.001 Å2-0.3348 Å2-0.0346 Å2--0.1856 Å2
L2.771 °21.3544 °20.2588 °2-2.1624 °20.1937 °2--1.0936 °2
S0.0643 Å °-0.0324 Å °0.0913 Å °-0.0095 Å °-0.0268 Å °0.1689 Å °-0.0759 Å °-0.2204 Å °-0.0038 Å °
Refinement TLS groupSelection details: ALL

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