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- PDB-3ab3: Crystal structure of p115RhoGEF RGS domain in complex with G alpha 13 -

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Basic information

Entry
Database: PDB / ID: 3ab3
TitleCrystal structure of p115RhoGEF RGS domain in complex with G alpha 13
Components
  • Guanine nucleotide-binding protein G(k) subunit alpha, Guanine nucleotide-binding protein subunit alpha-13
  • Rho guanine nucleotide exchange factor 1
KeywordsSIGNALING PROTEIN/MEMBRANE PROTEIN / SIGNAL TRANSDUCTION / PROTEIN COMPLEX / GTP-BINDING / MEMBRANE / TRANSDUCER / Lipoprotein / Nucleotide-binding / Palmitate / Phosphoprotein / GTPase activation / Guanine-nucleotide releasing factor / SIGNALING PROTEIN-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


D5 dopamine receptor binding / PLC beta mediated events / Adenylate cyclase inhibitory pathway / zymogen granule / CDC42 GTPase cycle / regulation of fibroblast migration / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / NRAGE signals death through JNK ...D5 dopamine receptor binding / PLC beta mediated events / Adenylate cyclase inhibitory pathway / zymogen granule / CDC42 GTPase cycle / regulation of fibroblast migration / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / NRAGE signals death through JNK / RAC1 GTPase cycle / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / Extra-nuclear estrogen signaling / G alpha (12/13) signalling events / positive regulation of NAD(P)H oxidase activity / vesicle fusion / G alpha (i) signalling events / negative regulation of vascular associated smooth muscle cell migration / GTP metabolic process / GTPase activating protein binding / regulation of small GTPase mediated signal transduction / dopamine receptor signaling pathway / branching involved in blood vessel morphogenesis / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of macroautophagy / negative regulation of apoptotic signaling pathway / Rho protein signal transduction / RHOA GTPase cycle / G protein-coupled serotonin receptor binding / positive regulation of vascular associated smooth muscle cell proliferation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / GTPase activator activity / guanyl-nucleotide exchange factor activity / positive regulation of superoxide anion generation / G protein-coupled receptor binding / brush border membrane / brain development / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / regulation of blood pressure / GDP binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / melanosome / midbody / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / angiogenesis / in utero embryonic development / cell differentiation / intracellular signal transduction / cell cycle / membrane raft / G protein-coupled receptor signaling pathway / cell division / protein domain specific binding / Golgi membrane / GTPase activity / centrosome / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / RNA binding / membrane / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p115RhoGEF, RGS domain / G-protein alpha subunit, group 12/13 / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / ARHGEF1-like, PH domain / PH domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like ...p115RhoGEF, RGS domain / G-protein alpha subunit, group 12/13 / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / ARHGEF1-like, PH domain / PH domain / 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. / G-protein alpha subunit, group I / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein subunit alpha-13 / Rho guanine nucleotide exchange factor 1 / Guanine nucleotide-binding protein G(i) subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKukimoto-Niino, M. / Mishima, C. / Shirouzu, M. / Kozasa, T. / Yokoyama, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Identification of critical residues in G(alpha)13 for stimulation of p115RhoGEF activity and the structure of the G(alpha)13-p115RhoGEF regulator of G protein signaling homology (RH) domain complex.
Authors: Hajicek, N. / Kukimoto-Niino, M. / Mishima-Tsumagari, C. / Chow, C.R. / Shirouzu, M. / Terada, T. / Patel, M. / Yokoyama, S. / Kozasa, T.
History
DepositionNov 30, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 1, 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(k) subunit alpha, Guanine nucleotide-binding protein subunit alpha-13
B: Rho guanine nucleotide exchange factor 1
C: Guanine nucleotide-binding protein G(k) subunit alpha, Guanine nucleotide-binding protein subunit alpha-13
D: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,16510
Polymers140,0244
Non-polymers1,1416
Water1,56787
1
A: Guanine nucleotide-binding protein G(k) subunit alpha, Guanine nucleotide-binding protein subunit alpha-13
B: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5825
Polymers70,0122
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-8 kcal/mol
Surface area24650 Å2
MethodPISA
2
C: Guanine nucleotide-binding protein G(k) subunit alpha, Guanine nucleotide-binding protein subunit alpha-13
D: Rho guanine nucleotide exchange factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5825
Polymers70,0122
Non-polymers5703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-10 kcal/mol
Surface area22810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.481, 70.640, 88.078
Angle α, β, γ (deg.)77.77, 84.45, 80.11
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Guanine nucleotide-binding protein G(k) subunit alpha, Guanine nucleotide-binding protein subunit alpha-13 / G-protein subunit alpha-13 / G alpha-13


Mass: 42363.418 Da / Num. of mol.: 2
Fragment: UNP RESIDUES 1-28 (G ALPHA I), UNP RESIDUES 47-377 (G ALPHA 13)
Source method: isolated from a genetically manipulated source
Details: ONE FUSED PROTEIN IS MADE OF RESIDUES 1-28 OF G ALPHA I, LINKER, AND RESIDUES 47-377 OF G ALPHA 13
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gna13, Gna-13 / Plasmid: PE060908-01 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9DC51, UniProt: P27601
#2: Protein Rho guanine nucleotide exchange factor 1 / 115 kDa guanine nucleotide exchange factor / p115-RhoGEF / p115RhoGEF / Sub1.5


Mass: 27648.441 Da / Num. of mol.: 2 / Fragment: N-TERMINAL RGS HOMOLOGY DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF1 / Plasmid: PE080111-02 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q92888

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Non-polymers , 4 types, 93 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CHAINS A AND C INCLUDE N-TERMINAL RESIDUES 1-28 OF G ALPHA I, LINKER (ARG-SER-ALA) AND RESIDUES ...THE CHAINS A AND C INCLUDE N-TERMINAL RESIDUES 1-28 OF G ALPHA I, LINKER (ARG-SER-ALA) AND RESIDUES 47-377 OF G ALPHA 13

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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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG 4000, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 37777 / % possible obs: 81.8 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 37.1 Å2 / Rsym value: 0.074 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.296 / % possible all: 82.1

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IAP, 1ZBC

1iap

1zbc


Resolution: 2.4→48.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1175586.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3734 10 %RANDOM
Rwork0.205 ---
obs0.205 37316 81.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.8937 Å2 / ksol: 0.360413 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.97 Å2-9.19 Å2-6.94 Å2
2--2 Å20.67 Å2
3----9.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8091 0 68 87 8246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d1.6
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 623 10.1 %
Rwork0.282 5571 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3ligand_xplor_paramligand_xplor_top
X-RAY DIFFRACTION4water.paramwater.top

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