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- PDB-1shz: Crystal Structure of the p115RhoGEF rgRGS Domain in A Complex wit... -

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Basic information

Entry
Database: PDB / ID: 1shz
TitleCrystal Structure of the p115RhoGEF rgRGS Domain in A Complex with Galpha(13):Galpha(i1) Chimera
Components
  • Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
  • Rho guanine nucleotide exchange factor 1
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / PROTEIN COMPLEX
Function / homology
Function and homology information


D5 dopamine receptor binding / regulation of fibroblast migration / CDC42 GTPase cycle / NRAGE signals death through JNK / Thromboxane signalling through TP receptor / Rho-activating G protein-coupled receptor signaling pathway / Extra-nuclear estrogen signaling / Thrombin signalling through proteinase activated receptors (PARs) / Adenylate cyclase inhibitory pathway / RAC1 GTPase cycle ...D5 dopamine receptor binding / regulation of fibroblast migration / CDC42 GTPase cycle / NRAGE signals death through JNK / Thromboxane signalling through TP receptor / Rho-activating G protein-coupled receptor signaling pathway / Extra-nuclear estrogen signaling / Thrombin signalling through proteinase activated receptors (PARs) / Adenylate cyclase inhibitory pathway / RAC1 GTPase cycle / G alpha (12/13) signalling events / positive regulation of phospholipase activity / branching involved in blood vessel morphogenesis / regulation of small GTPase mediated signal transduction / negative regulation of synaptic transmission / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / GTPase activating protein binding / G alpha (i) signalling events / RHOB GTPase cycle / NRAGE signals death through JNK / negative regulation of vascular associated smooth muscle cell migration / neurotransmitter receptor localization to postsynaptic specialization membrane / RHOC GTPase cycle / negative regulation of vascular associated smooth muscle cell proliferation / regulation of postsynapse assembly / Rho protein signal transduction / RHOA GTPase cycle / adenylate cyclase inhibitor activity / T cell migration / positive regulation of protein localization to cell cortex / in utero embryonic development / regulation of cell migration / D2 dopamine receptor binding / guanyl-nucleotide exchange factor activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / cellular response to forskolin / regulation of mitotic spindle organization / GTPase activator activity / chemokine-mediated signaling pathway / mast cell degranulation / brush border membrane / response to prostaglandin E / platelet activation / positive regulation of cholesterol biosynthetic process / regulation of blood pressure / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of cell shape / melanosome / GDP binding / positive regulation of cytosolic calcium ion concentration / heterotrimeric G-protein complex / G alpha (12/13) signalling events / angiogenesis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / midbody / G protein activity / cell cortex / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cell differentiation / postsynapse / intracellular signal transduction / G protein-coupled receptor signaling pathway / cell division / centrosome / GTPase activity / GTP binding / glutamatergic synapse / magnesium ion binding / protein-containing complex / RNA binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p115RhoGEF, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / G-protein alpha subunit, group 12/13 / ARHGEF1-like, PH domain / PH domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like ...p115RhoGEF, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / G-protein alpha subunit, group 12/13 / ARHGEF1-like, PH domain / PH domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / RGS, subdomain 2 / RGS domain superfamily / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Guanine nucleotide-binding protein subunit alpha-13 / Rho guanine nucleotide exchange factor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChen, Z. / Singer, W.D. / Sternweis, P.C. / Sprang, S.R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structure of the p115RhoGEF rgRGS domain-Galpha13/i1 chimera complex suggests convergent evolution of a GTPase activator.
Authors: Chen, Z. / Singer, W.D. / Sternweis, P.C. / Sprang, S.R.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 23, 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 / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_nonpoly_atom_coordination ...pdbx_entry_details / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / struct_conn
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
C: Rho guanine nucleotide exchange factor 1
D: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
F: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,11510
Polymers131,9744
Non-polymers1,1416
Water1,51384
1
A: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
C: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5585
Polymers65,9872
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-32 kcal/mol
Surface area25860 Å2
MethodPISA
2
D: Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera
F: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5585
Polymers65,9872
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-31 kcal/mol
Surface area25210 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-74 kcal/mol
Surface area47340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.747, 105.274, 71.748
Angle α, β, γ (deg.)90.00, 96.91, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe deposited PDB file contains a pair of homodimers of the complexes. However, the biological unit is identical to the monomeric form of the complex

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Components

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Protein , 2 types, 4 molecules ADCF

#1: Protein Guanine Nucleotide-Binding Protein Galpha(13):Galpha(i1) Chimera


Mass: 39640.191 Da / Num. of mol.: 2
Fragment: residues 21-47, 185-210, 213-230, 240-353 of Galpha(i1) and residues 64-207, 234-235, 254-262 of Galpha(13)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Genus: Mus, Rattus / Species: , / Strain: , / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P10824, UniProt: P27601
#2: Protein Rho guanine nucleotide exchange factor 1 / p115-RhoGEF / p115RhoGEF / 115 kDa guanine nucleotide exchange factor / Sub1.5


Mass: 26346.879 Da / Num. of mol.: 2
Fragment: N-terminal RhoGEF RGS (rgRGS) domain of p115RhoGEF (residues 7-239)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTrcC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92888

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Non-polymers , 4 types, 90 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium Sulfate, Tris, Ethylene glycol , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2003 / Details: MIRRORS
RadiationMonochromator: Double crystal, Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 33997 / Num. obs: 31348 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.188 / Net I/σ(I): 7.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 2286 / Rsym value: 0.585 / % possible all: 67.4

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AGR, CHAIN A

1agr


Resolution: 2.85→46.49 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1865632.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2203 7 %RANDOM
Rwork0.229 ---
obs0.229 31348 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.4754 Å2 / ksol: 0.30693 e/Å3
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.95 Å20 Å29.92 Å2
2---2.89 Å20 Å2
3----12.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.85→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8450 0 68 84 8602
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it3.721.5
X-RAY DIFFRACTIONc_mcangle_it5.742
X-RAY DIFFRACTIONc_scbond_it5.972
X-RAY DIFFRACTIONc_scangle_it8.412.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 251 6.5 %
Rwork0.333 3632 -
obs-3632 67.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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