PDB-2pbi: The multifunctional nature of Gbeta5/RGS9 revealed from its cryst...

ID or keywords:

Entry

Database: PDB / ID: 2pbi

Title

The multifunctional nature of Gbeta5/RGS9 revealed from its crystal structure

Components

Guanine nucleotide-binding protein subunit beta 5
Regulator of G-protein signaling 9

Keywords

SIGNALING PROTEIN / Helix wrap / RGS domain / DEP domain / DHEX domain / GGL domain / Beta propeller

Function / homology

Function and homology information

regulation of calcium ion export across plasma membrane / Inactivation, recovery and regulation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Adrenaline,noradrenaline inhibits insulin secretion ...regulation of calcium ion export across plasma membrane / Inactivation, recovery and regulation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / G beta:gamma signalling through BTK / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / light adaption / dark adaptation / G-protein gamma-subunit binding / G alpha (s) signalling events / Ca2+ pathway / G-protein activation / Extra-nuclear estrogen signaling / G alpha (12/13) signalling events / G alpha (q) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / GPER1 signaling / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cell tip / G alpha (i) signalling events / regulation of G protein-coupled receptor signaling pathway / GTPase activating protein binding / G protein-coupled dopamine receptor signaling pathway / parallel fiber to Purkinje cell synapse / negative regulation of signal transduction / photoreceptor outer segment / visual perception / photoreceptor inner segment / response to amphetamine / GTPase activator activity / postsynaptic density membrane / response to estradiol / myelin sheath / nervous system development / heterotrimeric G-protein complex / presynapse / protein-folding chaperone binding / signaling receptor complex adaptor activity / cell body / presynaptic membrane / postsynaptic membrane / neuron projection / intracellular signal transduction / G protein-coupled receptor signaling pathway / synapse / dendrite / glutamatergic synapse / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function

Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 - #60 / : / Regulator of G-protein signalling, DHEX domain / : / : / Regulator of G-protein signalling DHEX domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / Regulator of G-protein Signalling 4, domain 2 ...
Similarity search - Domain/homology

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 1.95 Å

Authors

Cheever, M.L. / Snyder, J.T. / Gershburg, S. / Siderovski, D.P. / Harden, T.K. / Sondek, J.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structure of the multifunctional Gbeta5-RGS9 complex.
Authors: Cheever, M.L. / Snyder, J.T. / Gershburg, S. / Siderovski, D.P. / Harden, T.K. / Sondek, J.

History

Deposition	Mar 28, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Derived calculations / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2pbi.cif.gz	642.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2pbi.ent.gz	527.3 KB	Display	PDB format
PDBx/mmJSON format	2pbi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pb/2pbi ftp://data.pdbj.org/pub/pdb/validation_reports/pb/2pbi	HTTPS FTP

-
Related structure data

Similar structure data	6i7d-2 1xr4-d 3oet-2 3oet-4 5djq-2 6vw1-1 6vzy-d 2hj0-d 4mv8-1 6qdj-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#58 - Oct 2004 G Proteins similarity (31) #60 - Dec 2004 Ubiquitin similarity (15) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (2) #217 - Jan 2018 Opioid Receptors similarity (2) #99 - Mar 2008 Cadherin similarity (1) #183 - Mar 2015 Phototropin similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (6)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#58 - Oct 2004
G Proteins
similarity (31)
#60 - Dec 2004
Ubiquitin
similarity (15)
#152 - Aug 2012
cAMP-dependent Protein Kinase
similarity (2)
#217 - Jan 2018
Opioid Receptors
similarity (2)
#99 - Mar 2008
Cadherin
similarity (1)
#183 - Mar 2015
Phototropin
similarity (2)
#126 - Jun 2010
Epidermal Growth Factor
similarity (1)
#164 - Aug 2013
Serotonin Receptor
similarity (6)

Deposited unit

A: Regulator of G-protein signaling 9

B: Guanine nucleotide-binding protein subunit beta 5

C: Regulator of G-protein signaling 9

D: Guanine nucleotide-binding protein subunit beta 5

hetero molecules

178 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Regulator of G-protein signaling 9

B: Guanine nucleotide-binding protein subunit beta 5

hetero molecules

defined by author&software
89.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Regulator of G-protein signaling 9

D: Guanine nucleotide-binding protein subunit beta 5

hetero molecules

defined by author&software
89.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.167, 119.032, 131.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Regulator of G-protein signaling 9 Mass: 49940.188 Da / Num. of mol.: 2 / Fragment: residues 1-422 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6J / Gene: Rgs9 / Plasmid: pFASTBacGST / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A1L352, UniProt: O54828*PLUS
#2: Protein	Guanine nucleotide-binding protein subunit beta 5 / Transducin beta chain 5 / Gbeta5 Mass: 38835.652 Da / Num. of mol.: 2 / Fragment: residues 43-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnb5 / Plasmid: pFASTBacHTb / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: P62881
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 890 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.5 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: MME PEG 550, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1
4		1
5		1
6		1

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARRESEARCH / Detector: CCD / Date: Oct 23, 2005

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Av σ(I) over netI	Number	R_merge(I) obs	Χ²	D res high (Å)	Num. obs	% possible obs
4.1	1	13.6	519790	0.075	1.34	1.95	125677	99.9
8.9	2	8.8	361943	0.108	1.25	2.8	40833	95
13.1	3	10.5	1054856	0.075	1.07	2.2	80767	92.6
12.8	4	10.5	966932	0.076	1.05	2.25	75389	92.4
13.2	5	10.7	820707	0.08	1.14	2.45	62072	96.7
9.3	6	8.7	329721	0.116	1.51	2.9	35553	90.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.2	50	99.6	1	0.06	1.581	4
3.33	4.2	100	1	0.059	1.867	4.2
2.91	3.33	100	1	0.069	1.96	4.2
2.65	2.91	100	1	0.078	1.533	4.2
2.46	2.65	100	1	0.097	1.336	4.2
2.31	2.46	100	1	0.13	1.228	4.2
2.2	2.31	99.9	1	0.171	1.132	4.1
2.1	2.2	99.8	1	0.222	0.959	4.1
2.02	2.1	99.7	1	0.295	0.894	4.1
1.95	2.02	99.7	1	0.434	0.886	4.1
6.03	50	98.3	2	0.072	2.113	9.4
4.79	6.03	99.2	2	0.078	1.551	9.7
4.18	4.79	99.6	2	0.071	1.262	9.8
3.8	4.18	99.8	2	0.091	1.126	9.8
3.53	3.8	99.9	2	0.135	1.135	9.8
3.32	3.53	100	2	0.198	1.052	9.8
3.15	3.32	99.9	2	0.296	0.979	9.4
3.02	3.15	97.5	2	0.406	0.937	8
2.9	3.02	86.6	2	0.47	0.903	6.2
2.8	2.9	69.1	2	0.518	0.915	5.3
4.74	50	100	3	0.054	1.502	14.5
3.76	4.74	100	3	0.054	1.487	15
3.29	3.76	100	3	0.069	1.287	15.1
2.99	3.29	100	3	0.105	1.014	15.1
2.77	2.99	100	3	0.178	0.911	15.1
2.61	2.77	100	3	0.278	0.836	14.7
2.48	2.61	99.9	3	0.35	0.777	12
2.37	2.48	90.3	3	0.384	0.758	9.2
2.28	2.37	74.9	3	0.41	0.754	8.1
2.2	2.28	60.2	3	0.46	0.748	7.8
4.85	50	100	4	0.05	1.289	14.5
3.85	4.85	100	4	0.05	1.335	15
3.36	3.85	100	4	0.072	1.3	15.1
3.05	3.36	100	4	0.117	1.034	15.1
2.83	3.05	100	4	0.208	0.903	15.1
2.67	2.83	100	4	0.338	0.847	14.6
2.53	2.67	100	4	0.433	0.807	11.7
2.42	2.53	92.3	4	0.48	0.785	8.3
2.33	2.42	73.4	4	0.534	0.797	7.4
2.25	2.33	57.7	4	0.588	0.804	6.9
5.28	50	100	5	0.052	1.375	14.4
4.19	5.28	100	5	0.051	1.378	14.9
3.66	4.19	100	5	0.07	1.56	15
3.32	3.66	100	5	0.099	1.311	15.1
3.09	3.32	100	5	0.169	1.041	15.1
2.9	3.09	100	5	0.285	0.909	15.1
2.76	2.9	100	5	0.425	0.859	14.3
2.64	2.76	99.5	5	0.533	0.824	11.1
2.54	2.64	92.8	5	0.555	0.845	8
2.45	2.54	74	5	0.614	0.888	7
6.24	50	99.8	6	0.085	3.468	10.3
4.96	6.24	100	6	0.094	1.791	10.9
4.33	4.96	99.9	6	0.09	1.495	11
3.94	4.33	100	6	0.111	1.236	11
3.65	3.94	100	6	0.156	1.147	10.4
3.44	3.65	99.2	6	0.193	1.027	9.2
3.27	3.44	93.5	6	0.267	0.908	8.3
3.12	3.27	83.9	6	0.344	0.846	7.3
3	3.12	72.4	6	0.423	0.796	6.1
2.9	3	58.6	6	0.47	0.781	5.2

Reflection

Resolution: 1.95→50 Å / Num. obs: 125677 / % possible obs: 99.9 % / Redundancy: 4.1 % / R_merge(I) obs: 0.075 / Χ²: 1.343 / Net I/σ(I): 13.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.95-2.02	4.1	0.434	12348	0.886	1	99.7
2.02-2.1	4.1	0.295	12398	0.894	1	99.7
2.1-2.2	4.1	0.222	12507	0.959	1	99.8
2.2-2.31	4.1	0.171	12430	1.132	1	99.9
2.31-2.46	4.2	0.13	12515	1.228	1	100
2.46-2.65	4.2	0.097	12553	1.336	1	100
2.65-2.91	4.2	0.078	12545	1.533	1	100
2.91-3.33	4.2	0.069	12614	1.96	1	100
3.33-4.2	4.2	0.059	12695	1.867	1	100
4.2-50	4	0.06	13072	1.581	1	99.6

-
Phasing

Phasing

Method:

MIRAS

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	44.19 Å
Translation	2.5 Å	44.19 Å

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 139878

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.52-100	70.9	0.816	1163
6.73-9.52	74.2	0.774	2105
5.5-6.73	75.8	0.792	2671
4.76-5.5	70.1	0.814	3121
4.26-4.76	65.8	0.803	3521
3.89-4.26	67.1	0.768	3893
3.6-3.89	67.5	0.745	4185
3.37-3.6	68.3	0.735	4499
3.17-3.37	69.5	0.738	4793
3.01-3.17	73.9	0.676	5047
2.87-3.01	75.2	0.621	5279
2.75-2.87	75.2	0.592	5533
2.64-2.75	76.3	0.593	5762
2.54-2.64	75.7	0.566	5977
2.46-2.54	75.8	0.539	6161
2.38-2.46	77.7	0.47	6432
2.31-2.38	78.5	0.421	6586
2.24-2.31	79.5	0.406	6746
2.18-2.24	86.4	0.314	6997
2.13-2.18	90.2	0.228	7065
2.08-2.13	89.5	0.268	7346
2.03-2.08	89.7	0.248	7450
1.98-2.03	90.3	0.273	7656
1.94-1.98	89	0.257	7778
1.9-1.94	89.7	0.238	7906
1.76-1.9	90	0.217	4206

-
Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
MLPHARE	CCP4_5.0	phasing
DM	5	phasing
REFMAC	refmac_5.2.0019	refinement
PDB_EXTRACT	2	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MIRAS / Resolution: 1.95→20 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	6300	5 %	RANDOM
R_work	0.183	-	-	-
obs	0.185	125475	99.68 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 37.882 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.82 Å²	0 Å²	0 Å²
2-	-	0.15 Å²	0 Å²
3-	-	-	0.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12255	0	54	890	13199

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	12716
X-RAY DIFFRACTION	r_angle_refined_deg	1.155	1.946	17200
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.863	5	1567
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.401	24.154	609
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.845	15	2257
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.176	15	79
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1823
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	9659
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	5648
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	8735
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	921
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.193	0.2	126
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.197	0.2	28
X-RAY DIFFRACTION	r_mcbond_it	0.501	1.5	7667
X-RAY DIFFRACTION	r_mcangle_it	0.932	2	12359
X-RAY DIFFRACTION	r_scbond_it	1.49	3	5049
X-RAY DIFFRACTION	r_scangle_it	2.297	4.5	4819

LS refinement shell

Resolution: 1.95→2.003 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.262	450	-
R_work	0.217	8395	-
obs	-	8845	96.95 %

-
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

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

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi