PDB-4fid: Crystal structure of a heterotrimeric G-Protein subunit from enta...

ID or keywords:

Entry

Database: PDB / ID: 4fid

Title

Crystal structure of a heterotrimeric G-Protein subunit from entamoeba histolytica, EHG-ALPHA-1

Components

G protein alpha subunit

Keywords

SIGNALING PROTEIN / RAS-LIKE DOMAIN / ALL-HELICAL DOMAIN / GTP BINDING /

NUCLEOTIDE BINDING /

TRANSDUCER /

LIPOPROTEIN / REDUCTIVE METHYLATION

Function / homology

Function and homology information

guanyl nucleotide binding / G protein-coupled receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway /

heterotrimeric G-protein complex /

GTPase activity
Similarity search - Function

Biological species

Entamoeba histolytica (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.62 Å

Authors

Bosch, D.E. / Kimple, A.J. / Muller, R.E. / Gigure, P.M. / Willard, F.S. / Machius, M. / Temple, B.R. / Siderovski, D.P.

Citation

Journal: Plos Pathog. / Year: 2012
Title: Heterotrimeric G-protein Signaling Is Critical to Pathogenic Processes in Entamoeba histolytica.
Authors: Bosch, D.E. / Kimple, A.J. / Muller, R.E. / Giguere, P.M. / Machius, M. / Willard, F.S. / Temple, B.R. / Siderovski, D.P.

History

Deposition	Jun 8, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2013	Group: Refinement description

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4fid.cif.gz	253.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4fid.ent.gz	216.6 KB	Display	PDB format
PDBx/mmJSON format	4fid.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fi/4fid ftp://data.pdbj.org/pub/pdb/validation_reports/fi/4fid	HTTPS FTP

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Related structure data

Similar structure data	1fqb-d 4z9l-d 1ez9-2 1git-d 2evh-d 1pfz-3 3ttk-1 5mkb-5 3oo9-2 6r38-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#58 - Oct 2004 G Proteins similarity (4) #251 - Nov 2020 Adenylyl Cyclase similarity (4) #147 - Mar 2012 Rhodopsin similarity (4) #164 - Aug 2013 Serotonin Receptor similarity (4) #60 - Dec 2004 Ubiquitin similarity (4)

Deposited unit

A: G protein alpha subunit

B: G protein alpha subunit

hetero molecules

78.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: G protein alpha subunit

hetero molecules

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

2

B: G protein alpha subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.671, 57.174, 231.289
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	G protein alpha subunit Mass: 38645.953 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-358 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM1:IMSS / Gene: EHG-ALPHA-1, EHI_140350 / Plasmid: PLIC-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: C4M483
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.26 %
Crystal grow	Temperature: 291 K / pH: 5.6 Details: EHG-ALPHA-1 AT 15 MG/ML IN CRYSTALLIZATION BUFFER (50 MM HEPES PH 6.5, 150 MM NACL, 10 MM MGCL2, 10 MM NAF, 30 MICROM ALCL3, AND 50 MICROM GDP) WAS MIXED 1:1 AND EQUILIBRATED AGAINST ...Details: EHG-ALPHA-1 AT 15 MG/ML IN CRYSTALLIZATION BUFFER (50 MM HEPES PH 6.5, 150 MM NACL, 10 MM MGCL2, 10 MM NAF, 30 MICROM ALCL3, AND 50 MICROM GDP) WAS MIXED 1:1 AND EQUILIBRATED AGAINST CRYSTALLIZATION SOLUTION CONTAINING 1.5 M AMMONIUM SULFATE, 175 MM K/NA TARTRATE, AND 100 MM SODIUM CITRATE PH 5.6. 250 MM AMMONIUM ACETATE WAS ADDED TO THE WELL SOLUTION AFTER SETTING THE DROPS, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

Crystal

Density Matthews: 2.42 Å³/Da / Density % sol: 49.26 %

Crystal grow

Temperature: 291 K / pH: 5.6
Details: EHG-ALPHA-1 AT 15 MG/ML IN CRYSTALLIZATION BUFFER (50 MM HEPES PH 6.5, 150 MM NACL, 10 MM MGCL2, 10 MM NAF, 30 MICROM ALCL3, AND 50 MICROM GDP) WAS MIXED 1:1 AND EQUILIBRATED AGAINST ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97954
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 5, 2011
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97954 Å / Relative weight: 1
Reflection	Resolution: 2.6→45.9 Å / Num. obs: 43503 / % possible obs: 99.3 % / Observed criterion σ(I): 1.37
Reflection shell	Resolution: 2.6→2.62 Å / Redundancy: 13.3 % / R_merge(I) obs: 0.982 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	AUTOSOL	model building
PHENIX	(PHENIX.REFINE: 1.6_289)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	AUTOSOL	phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.62→45.9 Å / SU ML: 0.35 / σ(F): 1.37 / Phase error: 25.32 / Stereochemistry target values: ML / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS

	R_factor	Num. reflection	% reflection
R_free	0.258	1172	4.95 %
R_work	0.189	-	-
obs	0.193	23398	99.3 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.47 Å² / k_sol: 0.35 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.6672 Å²	0 Å²	-0 Å²
2-	-	0.0515 Å²	0 Å²
3-	-	-	-2.7187 Å²

Refinement step

Cycle: LAST / Resolution: 2.62→45.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4900	0	56	39	4995

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5056
X-RAY DIFFRACTION	f_angle_d	1.205	6837
X-RAY DIFFRACTION	f_dihedral_angle_d	18.742	1869
X-RAY DIFFRACTION	f_chiral_restr	0.079	779
X-RAY DIFFRACTION	f_plane_restr	0.004	861

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.62-2.7102	0.3644	203	0.258	3956	X-RAY DIFFRACTION	94
2.7102-2.8187	0.342	218	0.2379	4118	X-RAY DIFFRACTION	100
2.8187-2.947	0.2807	217	0.2108	4133	X-RAY DIFFRACTION	100
2.947-3.1023	0.2836	208	0.2082	4208	X-RAY DIFFRACTION	100
3.1023-3.2967	0.2793	225	0.2127	4103	X-RAY DIFFRACTION	100
3.2967-3.5511	0.2645	220	0.1843	4210	X-RAY DIFFRACTION	100
3.5511-3.9083	0.2795	212	0.1726	4121	X-RAY DIFFRACTION	100
3.9083-4.4734	0.2321	215	0.1566	4194	X-RAY DIFFRACTION	100
4.4734-5.6344	0.1987	222	0.1568	4155	X-RAY DIFFRACTION	100
5.6344-45.9	0.2393	213	0.1936	4152	X-RAY DIFFRACTION	100

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	8.9918	-2.3017	4.7451	4.1137	0.6043	3.3283	-0.2911	-1.372	0.7386	0.2886	0.351	0.03	-0.2539	-1.2982	0.0058	0.1231	0.0896	-0.0007	0.1147	-0.0623	0.0593	4.582	10.3469	49.6306
2	0.8409	0.202	0.9024	0.7482	0.0838	4.2868	-0.1184	-0.1122	0.167	0.1598	-0.0424	0.1526	-0.5363	-0.2274	0.1367	0.1303	-0.0119	0.0456	0.0478	-0.0293	0.1298	20.7257	17.2258	71.6897
3	7.3481	-3.1603	4.8344	9.4808	-1.9635	3.1755	-0.4291	0.8997	0.6891	0.3421	0.031	-0.0039	-0.0404	0.4172	0.3612	0.2219	-0.1656	-0.016	0.2901	0.1584	0.2651	31.1011	18.9541	76.9766
4	0.4737	0.3755	-0.9078	1.7497	-2.9709	5.5927	-0.0333	-0.1828	-0.0691	-0.3704	-0.1796	-0.0362	0.5686	0.3616	0.1839	0.1415	0.0074	0.0189	0.1256	-0.0233	0.2634	26.0847	7.5322	72.4032
5	7.9715	2.2834	3.994	0.6548	1.155	6.3643	0.1182	-0.0461	0.8774	0.0213	-0.3645	0.0363	-1.2176	-0.0114	0.253	0.4167	-0.2331	-0.0368	0.2308	0.0206	0.4044	26.9709	26.8581	66.959
6	0.6554	-0.0894	0.8001	0.2308	-0.4847	1.6836	-0.9181	-0.1923	0.9236	0.1597	0.3012	-0.2303	-1.3469	-0.229	0.2222	0.1523	-0.1799	0.1025	-0.4797	0.0184	0.267	11.495	17.4232	51.6409
7	0.101	-1.1052	0.2609	1.998	-0.459	1.0521	-0.0123	-0.0769	-0.0807	0.0062	0.03	0.2762	0.0514	-0.1387	-0.0128	0.004	-0.0035	0.021	0.0819	0.0002	0.1978	6.3835	0.4282	56.9855
8	0.6231	0.1757	-1.2978	2.4421	-1.2175	2.0461	-0.0192	-0.0774	-0.0617	-0.3883	0.0744	-0.4948	0.1876	0.2594	-0.0742	0.1206	-0.0034	0.0428	0.1005	-0.1195	0.2506	14.1963	-9.3631	50.4215
9	5.0494	-2.6528	-5.5733	4.5687	1.2147	7.0892	-0.5888	-0.1918	0.3348	-0.3488	0.2185	0.8798	0.1918	0.6254	0.2027	0.1011	-0.0222	-0.1129	0.1101	-0.0061	0.303	8.0545	-2.887	42.9239
10	3.4468	-3.9383	0.9003	5.6429	-4.0941	8.551	0.748	0.0129	0.9692	-0.157	-0.8928	-0.7807	0.2783	1.3289	0.0897	0.1293	0.0219	0.1247	0.278	-0.0409	0.3337	20.0133	7.8444	48.6571
11	9.2901	-4.6801	-5.9976	4.0456	4.2711	4.7951	-0.4283	1.9133	-0.2496	0.1493	-0.5629	-0.0471	0.7839	-3.2121	1.0362	0.2842	0.0834	0.0598	0.7313	-0.051	0.1905	-4.1472	43.0399	101.7775
12	1.2498	-0.7302	-1.856	3.1861	2.232	2.2751	0.0816	0.5576	-0.1186	-0.1333	-0.3033	0.4223	-0.1174	-0.5669	0.2785	0.1984	-0.0935	-0.0247	0.4456	-0.0652	0.188	-0.3968	24.0018	95.2382
13	7.2583	0.6678	4.7094	0.318	1.6543	7.5724	-0.0128	0.3286	-0.8026	0.3599	0.0028	0.008	1.2079	0.1474	-0.0012	0.465	-0.0861	0.1304	0.1245	-0.0412	0.2078	18.4112	5.0231	87.9049
14	0.8194	-1.0978	-0.2107	0.8766	0.3597	0.847	-0.259	-0.0357	-0.2115	0.37	-0.1338	-0.166	0.6089	0.0051	0.4077	0.5127	-0.1867	0.2235	0.1854	-0.0736	0.2782	11.1503	8.1886	92.4642
15	1.2605	-1.161	-1.8192	4.5478	2.8801	2.2513	-0.1051	0.7727	-0.192	-0.0994	-0.5497	0.5713	-0.0686	-1.0774	0.604	0.2417	-0.1916	0.0641	0.5717	-0.1882	0.3305	-3.0735	23.9621	95.9401
16	4.2661	-4.183	-3.8786	4.0604	3.8041	4.7003	-1.5717	0.1941	-0.4247	0.3411	-0.163	0.5068	0.4328	-0.4273	0.9738	0.0575	-0.0557	0.4094	0.4861	0.1342	-0.6723	1.0876	39.4189	96.1778
17	8.563	-4.7585	-2.3927	2.7212	1.7845	2.3494	0.8909	-0.1742	1.033	-0.6709	-0.2268	-0.7016	-0.2287	-0.2239	-0.6213	0.3225	0.0009	0.1684	0.2214	-0.033	0.2978	4.5272	43.4529	100.1885
18	2.8349	0.7357	0.215	0.811	0.8481	1.1329	0.3187	0.362	0.1911	0.123	-0.0369	-0.0513	0.1542	0.013	-0.2215	0.2184	0.0025	0.0238	0.2711	-0.0439	0.2055	17.9993	31.438	104.9197
19	7.3949	-5.5681	-0.3532	4.7492	0.0982	0.077	-0.2776	-0.6761	0.8142	0.6072	0.0935	-0.744	0.2241	0.0448	0.0344	0.3394	0.0661	-0.1348	0.3055	-0.0585	0.2357	17.3954	35.9953	114.6774
20	0.4698	-0.711	0.2842	3.0704	-1.3483	0.6214	-0.1907	-0.3299	-0.1358	0.8451	0.2935	-0.0971	0.0428	-0.209	-0.0104	0.4325	-0.0616	0.0112	0.4105	0.0162	0.2248	4.7313	30.3271	111.1639

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND ( RESID 22:34 OR RESID 503:513 ) )	A	22 - 34
2	X-RAY DIFFRACTION	1	( CHAIN A AND ( RESID 22:34 OR RESID 503:513 ) )	A	503 - 513
3	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 35:107 )	A	35 - 107
4	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 108:113 )	A	108 - 113
5	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 114:144 )	A	114 - 144
6	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 145:154 )	A	145 - 154
7	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 155:184 )	A	155 - 184
8	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 185:274 )	A	185 - 274
9	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 275:303 )	A	275 - 303
10	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 318:323 )	A	318 - 323
11	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 324:337 )	A	324 - 337
12	X-RAY DIFFRACTION	11	( CHAIN B AND ( RESID 23:26 OR RESID 502:505 ) )	B	23 - 26
13	X-RAY DIFFRACTION	11	( CHAIN B AND ( RESID 23:26 OR RESID 502:505 ) )	B	502 - 505
14	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 27:69 )	B	27 - 69
15	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 70:95 )	B	70 - 95
16	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 96:147 )	B	96 - 147
17	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 148:180 )	B	148 - 180
18	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 181:198 )	B	181 - 198
19	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 199:209 )	B	199 - 209
20	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 210:274 )	B	210 - 274
21	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 275:318 )	B	275 - 318
22	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 319:335 )	B	319 - 335

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