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- PDB-1zca: Crystal structure of G alpha 12 in complex with GDP, Mg2+ and AlF4- -

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Basic information

Entry
Database: PDB / ID: 1zca
TitleCrystal structure of G alpha 12 in complex with GDP, Mg2+ and AlF4-
ComponentsG alpha i/12
KeywordsSIGNALING PROTEIN / GTP-binding / Lipoprotein / Membrane / Palmitate / Transducer
Function / homology
Function and homology information


D5 dopamine receptor binding / regulation of fibroblast migration / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / regulation of proteasomal ubiquitin-dependent protein catabolic process / response to xenobiotic stimulus => GO:0009410 / negative regulation of vascular associated smooth muscle cell migration / regulation of TOR signaling / embryonic digit morphogenesis / negative regulation of vascular associated smooth muscle cell proliferation ...D5 dopamine receptor binding / regulation of fibroblast migration / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / regulation of proteasomal ubiquitin-dependent protein catabolic process / response to xenobiotic stimulus => GO:0009410 / negative regulation of vascular associated smooth muscle cell migration / regulation of TOR signaling / embryonic digit morphogenesis / negative regulation of vascular associated smooth muscle cell proliferation / Rho protein signal transduction / lateral plasma membrane / G protein-coupled receptor binding / brush border membrane / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / regulation of cell shape / in utero embryonic development / cell differentiation / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
G-protein alpha subunit, group 12/13 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...G-protein alpha subunit, group 12/13 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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 / 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-12
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNance, M.R. / Tesmer, J.J.G.
CitationJournal: Biochemistry / Year: 2006
Title: A new approach to producing functional G alpha subunits yields the activated and deactivated structures of G alpha(12/13) proteins.
Authors: Kreutz, B. / Yau, D.M. / Nance, M.R. / Tanabe, S. / Tesmer, J.J. / Kozasa, T.
History
DepositionApr 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G alpha i/12
B: G alpha i/12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0468
Polymers83,9052
Non-polymers1,1416
Water1086
1
A: G alpha i/12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5234
Polymers41,9531
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: G alpha i/12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5234
Polymers41,9531
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.501, 85.230, 82.885
Angle α, β, γ (deg.)90.00, 106.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein G alpha i/12


Mass: 41952.535 Da / Num. of mol.: 2
Fragment: N-terminal residues 1-28 of G alpha i followed by residues 49-379 of G alpha 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pFastBacHTa / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P27600
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.3 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000 (14%), Sodium Citrate (100 mM), NaCl (50 mM), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2004 / Details: Si(111) double-crystal monochromator
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→29.1 Å / Num. all: 15297 / Num. obs: 15297 / % possible obs: 88.7 % / Redundancy: 2.2 % / Rsym value: 0.102 / Net I/σ(I): 6.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.67 / Num. unique all: 589 / Rsym value: 0.296

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZCB

1zcb


Resolution: 2.9→29.1 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.801 / SU B: 21.827 / SU ML: 0.402 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS refinement was utilizied.
RfactorNum. reflection% reflectionSelection details
Rfree0.29608 776 5.1 %RANDOM
Rwork0.23595 ---
all0.23895 ---
obs0.23895 14452 88.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.08 Å2
2---0.1 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5239 0 68 6 5313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225417
X-RAY DIFFRACTIONr_bond_other_d0.0010.024986
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.9677288
X-RAY DIFFRACTIONr_angle_other_deg0.699311577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475633
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4323.21271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.166151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2581548
X-RAY DIFFRACTIONr_chiral_restr0.0580.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021195
X-RAY DIFFRACTIONr_nbd_refined0.2160.21273
X-RAY DIFFRACTIONr_nbd_other0.160.25084
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22601
X-RAY DIFFRACTIONr_nbtor_other0.0790.23431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1540.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.68724176
X-RAY DIFFRACTIONr_mcbond_other0.05221288
X-RAY DIFFRACTIONr_mcangle_it0.81845116
X-RAY DIFFRACTIONr_scbond_it0.74642666
X-RAY DIFFRACTIONr_scangle_it1.13562172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1879tight positional0.010.05
3263medium positional0.210.5
1879tight thermal0.8210
3263medium thermal0.9210
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 45 -
Rwork0.351 806 -
obs-14452 68.41 %

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