PDB-2bt2: Structure of the regulator of G-protein signaling 16

ID or keywords:

Entry

Database: PDB / ID: 2bt2

Title

Structure of the regulator of G-protein signaling 16

Components

REGULATOR OF G-PROTEIN SIGNALING 16

Keywords

SIGNALING PROTEIN / GTPASE ACTIVATING PROTEIN / SIGNAL TRANSDUCTION INHIBITOR

Function / homology

Function and homology information

regulation of G protein-coupled receptor signaling pathway / positive regulation of GTPase activity / negative regulation of signal transduction / visual perception / GTPase activator activity / G alpha (z) signalling events / G alpha (i) signalling events / G alpha (q) signalling events / calmodulin binding / G protein-coupled receptor signaling pathway ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Bunkoczi, G. / Haroniti, A. / Longman, E. / Niesen, F. / Soundararajan, M. / Ball, L.J. / von Delft, F. / Doyle, D.A. / Arrowsmith, C. / Edwards, A. / Sundstrom, M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural Diversity in the Rgs Domain and its Interaction with Heterotrimeric G Protein Alpha- Subunits.
Authors: Soundararajan, M. / Willard, F.S. / Kimple, A.J. / Turnbull, A.P. / Ball, L.J. / Schoch, G.A. / Gileadi, C. / Fedorov, O.Y. / Dowler, E.F. / Higman, V.A. / Hutsell, S.Q. / Sundstrom, M. / ...

History

Deposition	May 25, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 3, 2005	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Aug 24, 2011	Group: Derived calculations / Structure summary
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2bt2.cif.gz	157.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2bt2.ent.gz	125.7 KB	Display	PDB format
PDBx/mmJSON format	2bt2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2bt2_validation.pdf.gz	474.1 KB	Display	wwPDB validaton report
Full document	2bt2_full_validation.pdf.gz	482 KB	Display
Data in XML	2bt2_validation.xml.gz	29.9 KB	Display
Data in CIF	2bt2_validation.cif.gz	43.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bt/2bt2 ftp://data.pdbj.org/pub/pdb/validation_reports/bt/2bt2	HTTPS FTP

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Related structure data

Related structure data	1zv4C 2a72C 2af0C 2bv1C 2es0C 2gtpC 2i59C 2ihbC 2ihdC 2ik8C 2jm5C 2jnuC 2odeC 2owiC 1agrS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1f32-d 3hmh-d 2kvz-d 1aal-d 2jrk-d 6y06-d 5c8q-d 3kz3-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) 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

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (5)

Deposited unit

A: REGULATOR OF G-PROTEIN SIGNALING 16

B: REGULATOR OF G-PROTEIN SIGNALING 16

C: REGULATOR OF G-PROTEIN SIGNALING 16

D: REGULATOR OF G-PROTEIN SIGNALING 16

E: REGULATOR OF G-PROTEIN SIGNALING 16

91.9 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: REGULATOR OF G-PROTEIN SIGNALING 16

defined by author&software
18.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: REGULATOR OF G-PROTEIN SIGNALING 16

defined by author&software
18.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: REGULATOR OF G-PROTEIN SIGNALING 16

defined by author&software
18.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: REGULATOR OF G-PROTEIN SIGNALING 16

defined by author&software
18.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: REGULATOR OF G-PROTEIN SIGNALING 16

defined by author&software
18.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	160.585, 31.743, 151.766
Angle α, β, γ (deg.)	90.00, 94.39, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-2052- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
1	2	A
2	2	C
3	2	D
1	3	B
2	3	E
1	4	A
2	4	B
3	4	C
4	4	D
5	4	E

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	54 - 140
2	1	1	4	B	54 - 140
3	1	1	4	C	54 - 140
4	1	1	4	D	54 - 140
5	1	1	4	E	54 - 140
1	2	1	4	A	149 - 188
2	2	1	4	B	149 - 188
3	2	1	4	C	149 - 188
4	2	1	4	D	149 - 188
5	2	1	4	E	149 - 188
1	1	2	4	A	130 - 149
2	1	2	4	C	130 - 149
3	1	2	4	D	130 - 149
1	1	3	4	B	130 - 149
2	1	3	4	E	130 - 149
1	1	4	4	A	45 - 54
2	1	4	4	B	45 - 54
3	1	4	4	C	45 - 54
4	1	4	4	D	45 - 54
5	1	4	4	E	45 - 54

NCS ensembles :

ID
1
2
3
4

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.99636, -0.01049, 0.08455), (-0.01063, 0.99994, -0.00115), (-0.08453, -0.00204, -0.99642)	-4.57949, 0.48144, 63.29848
3	given	(0.99921, 0.00472, -0.03934), (-0.00465, 0.99999, 0.0019), (0.03935, -0.00172, 0.99922)	2.14832, 2.44224, -31.47958
4	given	(0.9976, 0.00477, 0.06912), (-0.00444, 0.99998, -0.00485), (-0.06915, 0.00453, 0.9976)	-3.42816, -2.56613, 31.58353
5	given	(-0.99069, -0.01439, 0.13541), (-0.01313, 0.99986, 0.01015), (-0.13554, 0.00827, -0.99074)	-7.49536, -2.6761, 94.14874

#1: Protein	REGULATOR OF G-PROTEIN SIGNALING 16 / RGS16 / RETINALLY ABUNDANT REGULATOR OF G-PROTEIN SIGNALING / RGS-R / A28-RGS14P Mass: 18389.561 Da / Num. of mol.: 5 / Fragment: RESIDUES 53-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell: LYMPHOCYTE / Organ: LUNG, RETINA / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15492
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H₂O
Compound details	FUNCTION: INHIBITOR OF SIGNAL TRANSDUCTION

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 42 %
Crystal grow	pH: 5.5 / Details: 0.1 M BIS-TRIS, PH 5.5, 26% PEG3350, 0.1 M NH4AC

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.968
Detector	Type: MARRESEARCH / Detector: CCD / Date: Apr 23, 2005 / Details: MIRRORS
Radiation	Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.968 Å / Relative weight: 1
Reflection	Resolution: 1.9→44.23 Å / Num. obs: 216171 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.32 % / R_merge(I) obs: 0.08 / Net I/σ(I): 9.5
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 2.66 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2.39 / % possible all: 85.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AGR

1agr

Resolution: 1.9→30 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.934 / SU B: 8.698 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25	2980	5.1 %	RANDOM
R_work	0.192	-	-	-
obs	0.195	55845	95.6 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 28.88 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.48 Å²	0 Å²	0.34 Å²
2-	-	-1.27 Å²	0 Å²
3-	-	-	2.8 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5536	0	0	376	5912

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	5703
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5000
X-RAY DIFFRACTION	r_angle_refined_deg	1.404	1.933	7717
X-RAY DIFFRACTION	r_angle_other_deg	0.873	3	11567
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.563	5	720
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.241	24.022	276
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.645	15	935
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.784	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	849
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6470
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1265
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	1400
X-RAY DIFFRACTION	r_nbd_other	0.176	0.2	4762
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	2990
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	3156
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.218	0.2	335
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.162	0.2	34
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.165	0.2	131
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.173	0.2	28
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.258	3	3644
X-RAY DIFFRACTION	r_mcbond_other	1.477	3	1439
X-RAY DIFFRACTION	r_mcangle_it	4.251	5	5677
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.81	8	2311
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	9.207	11	2033
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1744	medium positional	0.36	0.5
1	2	B	1744	medium positional	0.39	0.5
1	3	C	1744	medium positional	0.34	0.5
1	4	D	1744	medium positional	0.39	0.5
1	5	E	1744	medium positional	0.45	0.5
2	1	A	296	medium positional	0.5	0.5
2	2	C	296	medium positional	0.58	0.5
2	3	D	296	medium positional	0.83	0.5
3	1	B	307	medium positional	0.3	0.5
4	1	A	88	medium positional	0.64	0.5
4	2	B	88	medium positional	0.63	0.5
4	3	C	88	medium positional	0.57	0.5
4	4	D	88	medium positional	0.88	0.5
4	5	E	88	medium positional	0.52	0.5
1	1	A	1744	medium thermal	1.21	2
1	2	B	1744	medium thermal	1.28	2
1	3	C	1744	medium thermal	1.21	2
1	4	D	1744	medium thermal	1.25	2
1	5	E	1744	medium thermal	1.28	2
2	1	A	296	medium thermal	0.98	2
2	2	C	296	medium thermal	0.95	2
2	3	D	296	medium thermal	1	2
3	1	B	307	medium thermal	1.01	2
4	1	A	88	medium thermal	1.13	2
4	2	B	88	medium thermal	0.86	2
4	3	C	88	medium thermal	1.32	2
4	4	D	88	medium thermal	0.84	2
4	5	E	88	medium thermal	0.99	2

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	193	-
R_work	0.265	3596	-
obs	-	-	84.33 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	14.0593	14.4718	-5.9795	15.053	-6.9432	6.5101	0.4051	-0.1517	-0.4074	0.3701	-0.1565	-0.1276	-0.4384	0.4788	-0.2486	-0.0369	-0.0455	0.0093	0.2912	-0.0259	0.1018	41.6275	39.3065	36.1921
2	2.6288	0.6312	-0.1552	1.9821	-0.537	1.6501	-0.0927	-0.0795	-0.1487	0.1817	0.0268	-0.2624	0.0369	0.1858	0.0659	-0.0646	0.0341	-0.0272	-0.1313	0.0082	-0.1599	14.0477	29.949	37.6407
3	1.6376	5.0163	2.3644	20.1635	4.7397	4.7192	-0.3223	0.5192	-0.6332	0.1395	0.66	-0.9642	-0.0862	0.6975	-0.3377	-0.0688	0.0892	0.0537	0.2285	0.0377	0.3628	39.7093	26.1164	34.8657
4	4.7472	-6.1631	-3.7086	14.0438	6.1353	4.4747	0.3743	0.237	0.2703	-0.3362	-0.2857	0.7184	-0.3225	-0.0254	-0.0886	-0.0417	0.1032	0.0141	0.2953	0.0881	0.2395	-43.8744	39.2957	24.3569
5	4.0498	0.604	-0.5133	2.0764	-0.1889	1.8156	-0.0343	0.0276	-0.198	-0.0752	-0.0421	0.0892	0.0755	-0.2365	0.0764	-0.0688	0.0321	-0.0056	-0.112	0.0193	-0.163	-15.5666	30.2205	24.4975
6	12.7584	-7.755	0.9349	7.4788	-5.2664	8.0512	0.0109	-0.2233	-0.3537	-0.3631	0.2074	0.6684	0.1247	-0.5909	-0.2184	-0.0667	-0.0949	-0.0051	0.2701	-0.0753	0.1218	-41.3861	25.8288	25.5221
7	4.702	8.6651	-2.5938	19.0992	-6.927	5.0464	0.3866	-0.1816	-0.1664	0.7441	0.0115	-0.4247	-0.5946	0.2	-0.398	-0.0512	-0.0946	0.0337	0.2039	-0.0339	0.0959	43.0271	42.1652	5.9186
8	2.8439	0.2595	-0.1697	1.4237	-0.2638	1.699	-0.0413	-0.0126	-0.1354	0.1172	-0.0253	-0.1956	0.0775	0.2055	0.0667	-0.0712	0.0143	0.0022	-0.1563	-0.002	-0.1866	14.7442	32.4069	6.6216
9	8.6334	7.7083	-1.0679	18.6295	5.2479	4.5267	-0.11	-0.028	-0.9678	-0.0329	0.0728	-1.4354	0.0834	0.7344	0.0372	-0.0705	0.1033	0.0261	0.1903	0.1217	0.1917	39.9193	27.0607	4.6888
10	19.1503	10.9588	-0.9454	24.777	-4.6521	0.9599	0.4694	1.1701	0.7222	0.5126	0.2647	-0.792	-0.0736	-0.3882	-0.734	0.0332	-0.1107	0.0888	0.5365	-0.1003	0.3979	40.3855	36.4446	65.3274
11	3.7618	-0.8762	-0.3303	3.8443	0.0867	1.6257	-0.047	-0.0634	-0.1007	0.2895	-0.0027	-0.2379	0.1043	0.1634	0.0497	-0.0224	0.0181	-0.045	-0.0589	0.0059	-0.1422	13.2048	27.1348	68.1855
12	6.8774	7.7646	-1.7015	12.7779	3.0629	6.6132	-0.2869	0.6619	-0.3881	-0.6957	0.2587	-1.1327	-0.3907	0.6783	0.0281	0.0769	0.1084	0.0288	0.3052	0.0147	0.3959	38.5101	22.9147	63.4642
13	14.5806	-7.1258	-3.9067	10.942	5.4367	2.7148	0.4628	0.8741	1.1115	-0.5431	-0.2587	-0.1518	-0.2529	-0.0491	-0.2041	0.0092	0.1619	0.0437	0.4326	0.1201	0.4742	-44.7961	36.355	53.4963
14	4.3293	0.5122	-0.0749	3.2581	0.1079	2.1547	-0.0667	-0.0422	-0.1699	0.0112	-0.0473	0.3017	0.0385	-0.2432	0.1141	-0.0477	0.0116	-0.0206	-0.0277	-0.0096	-0.1413	-16.3828	27.5539	55.2161
15	20.63	-14.759	-0.6792	33.2558	-7.3032	3.1756	0.3282	-1.151	-0.702	-0.5471	0.069	1.3456	0.3126	-0.9637	-0.3973	-0.0208	-0.1006	0.0132	0.5603	-0.0659	0.3299	-42.5418	23.1227	54.9015

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	46 - 60
2	X-RAY DIFFRACTION	2	A	61 - 172
3	X-RAY DIFFRACTION	3	A	173 - 188
4	X-RAY DIFFRACTION	4	B	46 - 60
5	X-RAY DIFFRACTION	5	B	61 - 172
6	X-RAY DIFFRACTION	6	B	173 - 187
7	X-RAY DIFFRACTION	7	C	45 - 60
8	X-RAY DIFFRACTION	8	C	61 - 172
9	X-RAY DIFFRACTION	9	C	173 - 186
10	X-RAY DIFFRACTION	10	D	47 - 60
11	X-RAY DIFFRACTION	11	D	61 - 172
12	X-RAY DIFFRACTION	12	D	173 - 187
13	X-RAY DIFFRACTION	13	E	45 - 60
14	X-RAY DIFFRACTION	14	E	61 - 172
15	X-RAY DIFFRACTION	15	E	173 - 187

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About Yorodumi

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Yorodumi