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- PDB-1b9y: STRUCTURAL ANALYSIS OF PHOSDUCIN AND ITS PHOSPHORYLATION-REGULATE... -

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Basic information

Entry
Database: PDB / ID: 1b9y
TitleSTRUCTURAL ANALYSIS OF PHOSDUCIN AND ITS PHOSPHORYLATION-REGULATED INTERACTION WITH TRANSDUCIN BETA-GAMMA
Components
  • (PROTEIN (TRANSDUCIN)) x 2
  • PROTEIN (PHOSDUCIN)
KeywordsSIGNALING PROTEIN / PHOSDUCIN / TRANSDUCIN / BETA-GAMMA / SIGNAL TRANSDUCTION / REGULATION / PHOSPHORYLATION / G PROTEINS / THIOREDOXIN / VISION / MEKA / COMPLEX (TRANSDUCER- TRANSDUCTION)
Function / homology
Function and homology information


Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma ...Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / eye photoreceptor cell development / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / regulation of G protein-coupled receptor signaling pathway / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction / photoreceptor outer segment / photoreceptor inner segment / visual perception / photoreceptor disc membrane / cellular response to catecholamine stimulus / intracellular protein localization / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / G protein-coupled receptor signaling pathway / GTPase activity / synapse / protein-containing complex binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Phosducin, domain 2 / Phosducin; domain 2 / Phosducin / Phosducin, N-terminal domain superfamily / : / Phosducin, thioredoxin-like domain / Phosducin / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Phosducin, domain 2 / Phosducin; domain 2 / Phosducin / Phosducin, N-terminal domain superfamily / : / Phosducin, thioredoxin-like domain / Phosducin / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Glutaredoxin / Glutaredoxin / Few Secondary Structures / Irregular / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / WD domain, G-beta repeat / Thioredoxin-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GADOLINIUM ATOM / Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Phosducin / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGaudet, R. / Sigler, P.B.
Citation
Journal: Mol.Cell / Year: 1999
Title: A molecular mechanism for the phosphorylation-dependent regulation of heterotrimeric G proteins by phosducin.
Authors: Gaudet, R. / Savage, J.R. / McLaughlin, J.N. / Willardson, B.M. / Sigler, P.B.
#1: Journal: Nature / Year: 1996
Title: Crystal structure of a G-protein beta gamma dimer at 2.1A resolution.
Authors: Sondek, J. / Bohm, A. / Lambright, D.G. / Hamm, H.E. / Sigler, P.B.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure at 2.4 angstroms resolution of the complex of transducin betagamma and its regulator, phosducin.
Authors: Gaudet, R. / Bohm, A. / Sigler, P.B.
History
DepositionFeb 16, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 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_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.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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: PROTEIN (TRANSDUCIN)
B: PROTEIN (TRANSDUCIN)
C: PROTEIN (PHOSDUCIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5779
Polymers73,6343
Non-polymers9446
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-91 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.470, 89.920, 102.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein PROTEIN (TRANSDUCIN) / GT BETA


Mass: 37430.957 Da / Num. of mol.: 1 / Fragment: LYS-C RESISTANT FRAGMENT, THE BETA SUBUNIT / Source method: isolated from a natural source / Details: PURIFIED FROM BOVINE ROD OUTER SEGMENTS / Source: (natural) Bos taurus (domestic cattle) / Cellular location: ROD OUTER SEGMENTS / Organ: EYE / Tissue: RETINA / References: UniProt: P62871
#2: Protein PROTEIN (TRANSDUCIN) / GT GAMMA


Mass: 8040.304 Da / Num. of mol.: 1
Fragment: LYS-C RESISTANT FRAGMENT, THE GAMMA SUBUNIT CLEAVED AFTER RESIDUE 68
Source method: isolated from a natural source / Details: PURIFIED FROM BOVINE ROD OUTER SEGMENTS / Source: (natural) Bos taurus (domestic cattle) / Cellular location: ROD OUTER SEGMENTS / Organ: EYE / Tissue: RETINA / References: UniProt: P02698
#3: Protein PROTEIN (PHOSDUCIN) / MEKA / PP33


Mass: 28162.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat)
Description: N-TERMINAL EXTENSION OF THE SEQUENCE MGSSHHHHHHSSGLVPRGSH.
Cellular location: CYTOSOLIC / Gene: RAT PDC / Organ: PINEAL GLAND, RETINA / Plasmid: PET15B/PHOSDUCIN / Species (production host): Escherichia coli / Gene (production host): RAT PDC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20942
#4: Chemical
ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Gd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPHOSPHORYLATION SITE S73 IN PHOSDUCIN IS PHOSPHORYLATED IN THIS STRUCTURE BUT IS NOT VISIBLE IN THE ...PHOSPHORYLATION SITE S73 IN PHOSDUCIN IS PHOSPHORYLATED IN THIS STRUCTURE BUT IS NOT VISIBLE IN THE ELECTRON DENSITY MAPS.

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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: 2.7 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CITRATE11
2MAGNESIUM ACETATE11
3PEG 800011
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.5 mMDTT1drop
325 mMsodium citrate1drop
475 mMmagnesium acetate1drop
54.75 %PEG80001drop
650 mMsodium citrate1reservoir
7150 mMmagnesium acetate1reservoir
89.5 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92
DetectorType: PRINCETON 2K / Detector: CCD / Date: Aug 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 13650 / Num. obs: 13650 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rsym value: 0.085 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.09 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.356 / % possible all: 97.1
Reflection
*PLUS
% possible obs: 94.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRC

2trc


Resolution: 3→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 329567.14 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2
Details: DISORDERED REGION IN PHOSDUCIN FROM RESIDUE 37 - 38 WAS MODELED STEREOCHEMICALLY AS A POLYALANINE CHAIN. DISORDERED REGION IN PHOSDUCIN FROM RESIDUE 39 - 86 WAS NOT VISIBLE IN THE MAPS AND WAS NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1240 9.7 %RANDOM
Rwork0.213 ---
obs-12803 88.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.58 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 67.9 Å2
Baniso -1Baniso -2Baniso -3
1--32.1 Å20 Å20 Å2
2---7.33 Å20 Å2
3---39.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 6 20 4527
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.74
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
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 160 9.3 %
Rwork0.288 1553 -
obs--70.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM.GDTOPO.GD
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 13650 / σ(F): 2 / % reflection Rfree: 9.7 % / Rfactor all: 0.224 / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 67.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.288 / Num. reflection obs: 1855 / Rfactor all: 0.33 / Rfactor obs: 0.288

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