[English] 日本語
Yorodumi
- PDB-1tbg: BETA-GAMMA DIMER OF THE HETEROTRIMERIC G-PROTEIN TRANSDUCIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tbg
TitleBETA-GAMMA DIMER OF THE HETEROTRIMERIC G-PROTEIN TRANSDUCIN
Components(TRANSDUCIN) x 2
KeywordsCOMPLEX (GTP-BINDING/TRANSDUCER) / COMPLEX (GTP-BINDING-TRANSDUCER) / EYE / TRANSDUCER / PRENYLATION / COMPLEX (GTP-BINDING-TRANSDUCER) 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 / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor ...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 / 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 disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / protein localization / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / signaling receptor complex adaptor activity / GTPase binding / retina development in camera-type eye / 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 / membrane / cytoplasm
Similarity search - Function
Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Few Secondary Structures / Irregular / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain ...Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / 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 / Mainly Beta
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(T) subunit gamma-T1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSondek, J.S. / Bohm, A. / Lambright, D.G. / Hamm, H.E. / Sigler, P.B.
Citation
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.
#1: Journal: Nature / Year: 1996
Title: The 2.0 A Crystal Structure of a Heterotrimeric G Protein
Authors: Lambright, D.G. / Sondek, J. / Bohm, A. / Skiba, N.P. / Hamm, H.E. / Sigler, P.B.
#2: 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.
#3: 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.
#4: Journal: Nature / Year: 1993
Title: The 2.2 A Crystal Structure of Transducin-Alpha Complexed with GTP Gamma S
Authors: Noel, J.P. / Hamm, H.E. / Sigler, P.B.
History
DepositionJun 15, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSDUCIN
E: TRANSDUCIN
B: TRANSDUCIN
F: TRANSDUCIN
C: TRANSDUCIN
G: TRANSDUCIN
D: TRANSDUCIN
H: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)181,5888
Polymers181,5888
Non-polymers00
Water13,187732
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: TRANSDUCIN
G: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-43 kcal/mol
Surface area17210 Å2
MethodPISA
3
B: TRANSDUCIN
F: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-40 kcal/mol
Surface area16940 Å2
MethodPISA
4
D: TRANSDUCIN
H: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-41 kcal/mol
Surface area17070 Å2
MethodPISA
5
A: TRANSDUCIN
E: TRANSDUCIN


Theoretical massNumber of molelcules
Total (without water)45,3972
Polymers45,3972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-40 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.100, 94.000, 194.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999339, -0.035733, 0.006634), (-0.034136, 0.985506, 0.166174), (-0.012475, 0.165838, -0.986074)125.72179, -17.47346, 236.6387
2given(-0.995922, 0.021439, 0.087635), (-0.036606, -0.983829, -0.17533), (0.082459, -0.177823, 0.980602)112.69596, 114.0073, 5.20845
3given(0.993596, -0.001803, -0.112978), (0.002097, -0.999406, 0.03439), (-0.112973, -0.034407, -0.993002)13.70356, 86.21671, 252.63943

-
Components

#1: Protein
TRANSDUCIN / GUANINE NUCLEOTIDE-BINDING PROTEIN G


Mass: 37416.930 Da / Num. of mol.: 4 / Fragment: BETA-1 SUBUNIT / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cell: ROD / Organ: EYE / Organelle: ROD OUTER SEGMENT / Tissue: RETINA / References: UniProt: P04901, UniProt: P62871*PLUS
#2: Protein
TRANSDUCIN / GUANINE NUCLEOTIDE-BINDING PROTEIN G


Mass: 7980.186 Da / Num. of mol.: 4 / Fragment: GAMMA-1 SUBUNIT / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cell: ROD / Organ: EYE / Organelle: ROD OUTER SEGMENT / Tissue: RETINA / References: UniProt: P02698
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 15-20 MG/ML PROTEIN MIXED 1:1 WITH WELL SOLUTION (10MM FUMARATE, PH 4.2, 10MM MGSO4, 2MM GDCL3, 5% W/V GLYCEROL, 5% W/V PEG 4000, 15MM BETA-MERCAPTOETHANOL. MIXTURE EQUILIBRATED VS. WELL ...Details: 15-20 MG/ML PROTEIN MIXED 1:1 WITH WELL SOLUTION (10MM FUMARATE, PH 4.2, 10MM MGSO4, 2MM GDCL3, 5% W/V GLYCEROL, 5% W/V PEG 4000, 15MM BETA-MERCAPTOETHANOL. MIXTURE EQUILIBRATED VS. WELL SOLUTION IN HANGING DROPS AT 4 DEGREES CELSIUS., vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 1:1 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
21 mMTris-HCl1drop
31 mM1dropMgCl2
45 mM1dropNaCl
515 mMbeta-mercaptoethanol1drop
65-7.5 %(v/v)glycerol1drop
710 mMfumarate1reservoir
810 mM1reservoirMgSO4
92 mM1reservoirGdCl3
105 %(v/v)glycerol1reservoir
115 %(v/v)PEG40001reservoir
1215 mMbeta-mercaptoethanol1reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 7, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionNum. obs: 88015 / % possible obs: 96 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. measured all: 258531

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.306 -
Rwork0.2 -
obs0.2 71169
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12541 0 0 732 13273
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_deg
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_improper_angle_deg1.4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more