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- PDB-3cx8: Crystal Structure of PDZRhoGEF rgRGS Domain in a Complex with Gal... -

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Basic information

Entry
Database: PDB / ID: 3cx8
TitleCrystal Structure of PDZRhoGEF rgRGS Domain in a Complex with Galpha-13 Bound to GTP-gamma-S
Components
  • Guanine nucleotide-binding protein alpha-13 subunit
  • Rho guanine nucleotide exchange factor 11
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / PROTEIN COMPLEX / GTP-binding / Lipoprotein / Membrane / Nucleotide-binding / Palmitate / Phosphoprotein / Transducer / Coiled coil / Cytoplasm / GTPase activation / Guanine-nucleotide releasing factor
Function / homology
Function and homology information


Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / CDC42 GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / CDC42 GTPase cycle / RAC1 GTPase cycle / NRAGE signals death through JNK / Thromboxane signalling through TP receptor / regulation of fibroblast migration ...Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / CDC42 GTPase cycle / NRAGE signals death through JNK / G alpha (12/13) signalling events / CDC42 GTPase cycle / RAC1 GTPase cycle / NRAGE signals death through JNK / Thromboxane signalling through TP receptor / regulation of fibroblast migration / Rho-activating G protein-coupled receptor signaling pathway / RHOA GTPase cycle / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of L-glutamate import across plasma membrane / RAC1 GTPase cycle / G alpha (12/13) signalling events / branching involved in blood vessel morphogenesis / negative regulation of vascular associated smooth muscle cell migration / negative regulation of vascular associated smooth muscle cell proliferation / regulation of postsynapse assembly / Rho protein signal transduction / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / platelet activation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / melanosome / heterotrimeric G-protein complex / regulation of cell shape / G protein activity / angiogenesis / in utero embryonic development / cell differentiation / postsynapse / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / positive regulation of DNA-templated transcription / GTP binding / metal ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, 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 ...Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, 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 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / 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. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / 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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Guanine nucleotide-binding protein subunit alpha-13 / Rho guanine nucleotide exchange factor 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSprang, S.R. / Chen, Z.
CitationJournal: Structure / Year: 2008
Title: Recognition of the Activated States of Galpha13 by the rgRGS Domain of PDZRhoGEF.
Authors: Chen, Z. / Singer, W.D. / Danesh, S.M. / Sternweis, P.C. / Sprang, S.R.
History
DepositionApr 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein alpha-13 subunit
B: Rho guanine nucleotide exchange factor 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6304
Polymers63,0672
Non-polymers5642
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-26 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.109, 66.117, 152.521
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 Guanine nucleotide-binding protein alpha-13 subunit / G alpha-13


Mass: 39743.516 Da / Num. of mol.: 1 / Fragment: N-terminally truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gna13, Gna-13 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27601
#2: Protein Rho guanine nucleotide exchange factor 11 / RhoGEF glutamate transport modulator GTRAP48


Mass: 23323.350 Da / Num. of mol.: 1 / Fragment: RhoGEF-RGS (rgRGS) Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef11 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ES67
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17-24 % polyethylene glycol 8000 and 100 mM Na+ HEPES, pH 7.3-7.8, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2007 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 40370 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.092 / Net I/σ(I): 22.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.467 / % possible all: 90.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
PHASERphasing
RefinementStarting model: PDB Entry 1ZCB, 1HTJ

1zcb

1htj


Resolution: 2→40 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4000 9.9 %Random
Rwork0.223 ---
all0.243 40516 --
obs0.243 39804 98.2 %-
Solvent computationBsol: 39.525 Å2
Displacement parametersBiso mean: 32.504 Å2
Baniso -1Baniso -2Baniso -3
1--1.325 Å20 Å20 Å2
2--0.766 Å20 Å2
3---0.559 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 33 298 4513
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.306
X-RAY DIFFRACTIONc_mcbond_it1.4221.5
X-RAY DIFFRACTIONc_scbond_it2.3372
X-RAY DIFFRACTIONc_mcangle_it2.1812
X-RAY DIFFRACTIONc_scangle_it3.6192.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION4GTPgS.paramGTPgS.top

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