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- PDB-2trc: PHOSDUCIN/TRANSDUCIN BETA-GAMMA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2trc
TitlePHOSDUCIN/TRANSDUCIN BETA-GAMMA COMPLEX
Components
  • (TRANSDUCIN) x 2
  • PHOSDUCIN
KeywordsCOMPLEX (TRANSDUCER/TRANSDUCTION) / PHOSDUCIN / TRANSDUCIN / BETA-GAMMA / SIGNAL TRANSDUCTION / REGULATION / PHOSPHORYLATION / G PROTEINS / THIOREDOXIN / VISION / MEKA / COMPLEX (TRANSDUCER-TRANSDUCTION) / COMPLEX (TRANSDUCER-TRANSDUCTION) complex
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 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / response to stimulus / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / phototransduction / photoreceptor outer segment / photoreceptor inner segment / visual perception / protein localization / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / 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 / protein-containing complex binding / membrane / nucleus / cytosol / cytoplasm
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 / 7 Propeller ...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 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / Glutaredoxin / G-protein, beta subunit / Glutaredoxin / Few Secondary Structures / Irregular / Thioredoxin-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsGaudet, R. / Bohm, A. / Sigler, P.B.
Citation
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.
#1: Journal: Nature / Year: 1996
Title: Crystal Structure of a Ga Protein Beta Gamma Dimer at 2.1A Resolution
Authors: Sondek, J. / Bohm, A. / Lambright, D.G. / Hamm, H.E. / Sigler, P.B.
History
DepositionJan 6, 1997Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification ..._pdbx_database_status.process_site / _software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: TRANSDUCIN
G: TRANSDUCIN
P: PHOSDUCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3468
Polymers70,5603
Non-polymers7865
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10920 Å2
ΔGint-88 kcal/mol
Surface area27150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.700, 88.510, 98.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSDUCIN / GT BETA-GAMMA


Mass: 37430.957 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 (cattle) / Cell line: B834 / Cellular location: ROD OUTER SEGMENTS / Organ: EYE / Tissue: RETINA / References: UniProt: P62871
#2: Protein TRANSDUCIN / GT BETA-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 (cattle) / Cell line: B834 / Cellular location: ROD OUTER SEGMENTS / Organ: EYE / Tissue: RETINA / References: UniProt: P02698
#3: Protein PHOSDUCIN / / MEKA / PP33


Mass: 25088.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: ZIVIC-MILLER SPRAGUE-DAWLEY / Tissue: RETINA / Cell line: B834 / Cellular location: CYTOSOLICCytosol / Organ: PINEAL GLAND, RETINA / References: UniProt: P20942
#4: Chemical
ChemComp-GD / GADOLINIUM ATOM


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.7 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: THE PROTEIN COMPLEX (10 MG/ML SOLUTION) WAS CRYSTALLIZED FROM 50 MM SODIUM CITRATE (PH 5.0), 150 MM MAGNESIUM ACETATE, 9.5% PEG 8000, BY HANGING DROP METHOD AT 4 DEGREES C., vapor diffusion - ...Details: THE PROTEIN COMPLEX (10 MG/ML SOLUTION) WAS CRYSTALLIZED FROM 50 MM SODIUM CITRATE (PH 5.0), 150 MM MAGNESIUM ACETATE, 9.5% PEG 8000, BY HANGING DROP METHOD AT 4 DEGREES C., vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
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: NSLS / Beamline: X4A / Wavelength: 0.9791 / Wavelength: 0.9791, 1.7109
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 6, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21.71091
ReflectionResolution: 2.4→50 Å / Num. obs: 24085 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 37 Å2 / Rsym value: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.37→2.44 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.301 / % possible all: 97
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 96.8 % / Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
X-PLOR3.8model building
SHELXrefinement
SHELXmodel building
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.0057 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: DISORDERED REGION IN PHOSDUCIN FROM RESIDUE 37 - 66 WAS MODELED STEREOCHEMICALLY AS A POLYALANINE CHAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2358 9.8 %RANDOM
Rwork0.19 ---
obs0.19 24085 91.4 %-
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--12.102 Å20 Å20 Å2
2---25.642 Å20 Å2
3----29.316 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 5 234 5070
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.8911.5
X-RAY DIFFRACTIONx_mcangle_it4.8532
X-RAY DIFFRACTIONx_scbond_it4.3992
X-RAY DIFFRACTIONx_scangle_it6.9142.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 234 7.14 %
Rwork0.233 2195 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2SOLVENT.PARAMTOPOLOGY.ELEMENTS
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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