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- PDB-1tad: GTPASE MECHANISM OF GPROTEINS FROM THE 1.7-ANGSTROM CRYSTAL STRUC... -

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Basic information

Entry
Database: PDB / ID: 1tad
TitleGTPASE MECHANISM OF GPROTEINS FROM THE 1.7-ANGSTROM CRYSTAL STRUCTURE OF TRANSDUCIN ALPHA-GDP-ALF4-
ComponentsTRANSDUCIN-ALPHA
KeywordsGTP-BINDING PROTEIN / G-PROTEIN / GTPASE / TRANSDUCIN
Function / homology
Function and homology information


negative regulation of cyclic-nucleotide phosphodiesterase activity / detection of light stimulus involved in visual perception / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / photoreceptor outer segment membrane / G alpha (i) signalling events / acyl binding / response to light stimulus / phototransduction, visible light ...negative regulation of cyclic-nucleotide phosphodiesterase activity / detection of light stimulus involved in visual perception / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / photoreceptor outer segment membrane / G alpha (i) signalling events / acyl binding / response to light stimulus / phototransduction, visible light / phototransduction / photoreceptor inner segment / G protein-coupled receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G-protein beta/gamma-subunit complex binding / photoreceptor disc membrane / GDP binding / heterotrimeric G-protein complex / GTPase activity / protein kinase binding / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold ...GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / G-protein alpha subunit, group I / 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 / 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 / CACODYLATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(t) subunit alpha-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsSondek, J. / Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B.
Citation
Journal: Nature / Year: 1994
Title: GTPase mechanism of Gproteins from the 1.7-A crystal structure of transducin alpha-GDP-AIF-4.
Authors: Sondek, J. / Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B.
#1: Journal: Nature / Year: 1994
Title: Structural Determinants for Activation of the Alpha-Subunit of a Heterotrimeric G Protein
Authors: Lambright, D.G. / Noel, J.P. / Hamm, H.E. / Sigler, P.B.
#2: Journal: Nature / Year: 1993
Title: The 2.2 Angstroms Crystal Structure of Transducin-Alpha Complexed with GTP-Gamma-S
Authors: Noel, J.P. / Hamm, H.E. / Sigler, P.B.
History
DepositionJan 5, 1995Processing site: BNL
Revision 1.0May 8, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: TRANSDUCIN-ALPHA
B: TRANSDUCIN-ALPHA
C: TRANSDUCIN-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,00518
Polymers111,4243
Non-polymers2,58115
Water18,2671014
1
C: TRANSDUCIN-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0026
Polymers37,1411
Non-polymers8605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRANSDUCIN-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0026
Polymers37,1411
Non-polymers8605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: TRANSDUCIN-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0026
Polymers37,1411
Non-polymers8605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.900, 108.200, 79.000
Angle α, β, γ (deg.)90.00, 111.70, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES CAC A 353, CAC B 353, AND CAC C 353 MODIFY RESIDUES CYS A 62, CYS B 62, AND CYS C 62, RESPECTIVELY.
2: RESIDUES CAC A 354, CAC B 354, AND CAC C 354 MODIFY RESIDUES CYS A 210, CYS B 210, AND CYS C 210, RESPECTIVELY.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.108857, -0.734399, 0.669931), (0.740433, -0.509567, -0.438291), (0.663255, 0.448328, 0.599244)-0.14894, 122.4098, -67.93221
2given(-0.025413, 0.728142, 0.684955), (-0.770147, -0.45111, 0.450974), (0.637359, -0.51606, 0.572241)-92.19028, 89.60443, 28.33287
3given(-0.075158, -0.69048, 0.719434), (0.71881, -0.53756, -0.440838), (0.691132, 0.484, 0.536728)41.19659, 125.4493, 5.41535
DetailsTHERE ARE THREE COMPLEXES OF TRANSDUCIN ALPHA, GDP, ALUMINUM FLUORIDE, AND CA 2+ PER ASYMMETRIC UNIT. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 C 30 .. C 340 B 30 .. B 340 0.252 M2 C 30 .. C 340 A 30 .. A 340 0.353 M3 B 30 .. B 340 A 30 .. A 340 0.404

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein TRANSDUCIN-ALPHA


Mass: 37141.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: RETINA / Organ: EYE / References: UniProt: P04695

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Non-polymers , 5 types, 1029 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1014 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCAC IS DIMETHYL ARSENIC OXIDE, DERIVED FROM CRYSTALLIZATION BUFFER. ALSO KNOWN AS DIMETHYLARSINIC ...CAC IS DIMETHYL ARSENIC OXIDE, DERIVED FROM CRYSTALLIZATION BUFFER. ALSO KNOWN AS DIMETHYLARSINIC ACID AND CACODYLIC ACID.

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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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein11
220 %(w/v)PEG800011
3200 mM11CaCl2
4100 mMsodium cacodylate11
50.2 %(v/v)beta-mercaptoethanol11
65 mM11MgCl2
70.1 M11AlCl3
830 mM11NaF
940 %(v/v)glycerol11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 11, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionNum. obs: 116584 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.1
Reflection
*PLUS
Highest resolution: 1.7 Å / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.78 Å / % possible obs: 76.7 % / Redundancy: 4.22 % / Num. unique obs: 12535 / Rmerge(I) obs: 0.186

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.7→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.266 -
Rwork0.209 -
obs0.209 116584
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7633 0 126 1014 8773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor all: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS

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