PDB-8vga: Crystal Structure of Guanine Nucleotide-Binding Protein (G Protei...

ID or keywords:

Entry

Database: PDB / ID: 8vga

Title

Crystal Structure of Guanine Nucleotide-Binding Protein (G Protein) Alpha-1 Subunit from Selaginella moellendorffii in complex with GTP gamma S

Components

Guanine nucleotide-binding protein alpha subunit

Keywords

SIGNALING PROTEIN / G Protein / Alpha Subunit / SmGPA1 / elaginella moellendorffii

Function / homology

Function and homology information

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 / GTP binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Selaginella moellendorffii (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.57602485808 Å

Authors

Lee, S.G. / Jez, J.M.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2024
Title: Structure-function analysis of plant G-protein regulatory mechanisms identifies key G alpha-RGS protein interactions.
Authors: Torres-Rodriguez, M.D. / Lee, S.G. / Roy Choudhury, S. / Paul, R. / Selvam, B. / Shukla, D. / Jez, J.M. / Pandey, S.

History

Deposition	Dec 27, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vga.cif.gz	353.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8vga.ent.gz	240.9 KB	Display	PDB format
PDBx/mmJSON format	8vga.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vga_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8vga_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8vga_validation.xml.gz	30.7 KB	Display
Data in CIF	8vga_validation.cif.gz	40.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vg/8vga ftp://data.pdbj.org/pub/pdb/validation_reports/vg/8vga	HTTPS FTP

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Related structure data

Related structure data	8vgbC C: citing same article (ref.)
Similar structure data	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 (7) #251 - Nov 2020 Adenylyl Cyclase similarity (6) #147 - Mar 2012 Rhodopsin similarity (5) #164 - Aug 2013 Serotonin Receptor similarity (5) #60 - Dec 2004 Ubiquitin similarity (5)

Deposited unit

A: Guanine nucleotide-binding protein alpha subunit

B: Guanine nucleotide-binding protein alpha subunit

hetero molecules

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

1

A: Guanine nucleotide-binding protein alpha subunit

hetero molecules

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

2

B: Guanine nucleotide-binding protein alpha subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.055, 61.468, 111.871
Angle α, β, γ (deg.)	90.000, 115.230, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Guanine nucleotide-binding protein alpha subunit / GP-alpha Mass: 43275.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selaginella moellendorffii (plant) / Gene: GPA-1, SELMODRAFT_449882 / Production host: Escherichia coli (E. coli) / References: UniProt: D8QR00
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.92 Å³/Da / Density % sol: 68.61 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 20% (w/v) polyethylene glycol (PEG)-3350, 200 mM potassium citrate tribasic

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.57→50 Å / Num. obs: 42607 / % possible obs: 99.8 % / Redundancy: 3.7 % / B_iso Wilson estimate: 48.2797466139 Å² / R_pim(I) all: 0.069 / R_rim(I) all: 0.133 / R_sym value: 0.084 / Net I/σ(I): 16.6
Reflection shell	Resolution: 2.57→2.61 Å / Mean I/σ(I) obs: 2.01 / Num. unique obs: 2086 / CC_1/2: 0.616 / R_pim(I) all: 0.474 / R_rim(I) all: 0.916 / R_sym value: 0.782

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
HKL-3000	1.11.1_2575	data collection
PHASER		phasing
Coot		model building
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.57602485808→42.6224322563 Å / SU ML: 0.318511652908 / Cross valid method: FREE R-VALUE / σ(F): 1.34361512083 / Phase error: 22.7555571939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.216388308106	2002	4.71103162651 %
R_work	0.175021871076	40494	-
obs	0.176964721126	42496	99.141470698 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 58.4192866655 Å²

Refinement step

Cycle: LAST / Resolution: 2.57602485808→42.6224322563 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5491	0	66	148	5705

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.00773026937147	5688
X-RAY DIFFRACTION	f_angle_d	0.913262917175	7698
X-RAY DIFFRACTION	f_chiral_restr	0.053756921748	837
X-RAY DIFFRACTION	f_plane_restr	0.00467820703055	979
X-RAY DIFFRACTION	f_dihedral_angle_d	4.4004843456	4082

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 (%)
2.58-2.6404	0.30901959486	125	0.263623023799	2607	X-RAY DIFFRACTION	90.5235255136
2.6404-2.7118	0.265424334762	148	0.25114474636	2890	X-RAY DIFFRACTION	99.8685075608
2.7118-2.7916	0.304964183647	142	0.239873001849	2933	X-RAY DIFFRACTION	99.9025341131
2.7916-2.8817	0.280149084203	138	0.209789313661	2861	X-RAY DIFFRACTION	99.9333555482
2.8817-2.9847	0.237003683913	149	0.19541270982	2882	X-RAY DIFFRACTION	99.9670184697
2.9847-3.1041	0.224715218734	140	0.202596216916	2941	X-RAY DIFFRACTION	99.9675535367
3.1041-3.2453	0.27023642483	144	0.207849600691	2860	X-RAY DIFFRACTION	99.9667221298
3.2453-3.4164	0.236525556315	147	0.19508807677	2932	X-RAY DIFFRACTION	99.935086011
3.4164-3.6303	0.242084445126	139	0.182354616396	2899	X-RAY DIFFRACTION	99.8356884653
3.6303-3.9104	0.205386575685	147	0.16320752619	2896	X-RAY DIFFRACTION	99.7377908882
3.9104-4.3036	0.186316511567	141	0.148826847479	2915	X-RAY DIFFRACTION	99.6738421396
4.3036-4.9256	0.176312474346	143	0.134024134413	2913	X-RAY DIFFRACTION	99.5115597525
4.9256-6.2027	0.178072360737	146	0.170341570821	2951	X-RAY DIFFRACTION	99.6460746461
6.2027-42.62	0.204682719882	153	0.152172293398	3014	X-RAY DIFFRACTION	99.4036409291

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	8.04426209465	-0.232952628265	0.376037621281	6.55022904339	2.16356755516	6.48051548663	-0.098845304629	0.935631213899	-0.0801682767364	-0.655979257645	0.0936285246568	-0.236183071252	0.097655153862	0.101729244944	-0.0768005515366	0.372422903808	-0.0544082714499	-0.00414596043008	0.372214510599	0.0453630924964	0.389114391756	157.231381966	0.677790709861	140.037132863
2	5.48409920075	2.23635981239	1.41098036395	3.11307905635	1.14921818433	6.89550152129	-0.181711522984	-0.297151947906	-0.2284595332	-0.0646164026344	0.194804281742	-0.367866844979	-0.532879972635	0.581262552495	-0.0231624675258	0.369488312206	0.0383815707791	0.127975600399	0.466751710174	0.0940755770696	0.56738925805	184.986940667	9.78666712007	149.517097292
3	4.64695370314	1.04665473332	-1.11780343339	1.8039410299	0.235395378392	8.60633218494	-0.210933844737	-0.306604102083	-0.491473457914	0.0395778846939	-0.0487337101973	-0.112085490708	0.00304663488951	0.235208205682	0.208330367073	0.287322343176	0.0517949289436	0.0702540542539	0.354660377976	0.126664472395	0.702832915385	183.821152351	4.92981476736	148.239723688
4	4.45569826351	-0.141685104949	-1.57832818559	2.06318469773	-0.660711878831	3.95605490821	-0.269686364044	0.541369089753	-0.380782724997	-0.296083876589	0.0510478620508	-0.0551666590712	0.0857058510074	0.307864029344	-0.0141674607353	0.398504870969	-0.109796899264	0.104144677893	0.498430850092	-0.0414595886028	0.693794931105	175.365197377	2.31994896684	137.777063722
5	4.12639766562	-1.07474943485	-0.652890517639	2.94834195554	0.336305961093	5.05353940693	0.164594815924	0.361665011447	0.225804185635	-0.377154613333	0.0677242278881	0.0429235148022	-0.182547002292	-0.414719537513	-0.0746739933585	0.330170053929	0.00580402227321	-0.0657047149243	0.3039156063	0.0242781148641	0.491932878431	152.88237305	5.6478023336	144.457891863
6	4.48994382091	-1.31182867852	-0.276412701411	5.97948977215	0.0638835566879	2.82238918443	-0.231255595833	-0.533760753196	0.10779846794	0.797167314638	0.212800725694	-0.580949257463	0.0925960330395	0.290652443245	0.00314491021373	0.382740412938	0.0267331394891	-0.0748603306	0.327053280899	-0.0243462932054	0.457218834754	160.419968701	-0.0998594960499	160.723678728
7	8.61716047563	-2.46026820249	2.30711007007	6.04347634005	-1.52516629044	3.39324767971	-0.624942754721	-0.354221258394	-0.754818523957	1.48698024819	0.385046590803	0.113503837437	0.616366840949	-0.208140392585	-0.0255662575884	0.561420931739	0.0225718734761	-0.0137820285598	0.345835067264	0.0393522037684	0.405971052832	156.650101012	-9.12702577928	163.191427476
8	3.37337739092	2.45521604345	0.24075514842	6.33606797321	0.916497044962	3.88081855791	0.064900855673	0.0898303836684	0.0628737020716	-0.292908725866	0.0688167348158	0.181973617009	-0.0196118214223	-0.0508714473392	-0.183819933728	0.28769121159	-0.0085593051047	-0.0188629401752	0.205127433467	0.042818228307	0.42265710476	150.405105695	-9.07768344147	148.821650977
9	5.44026158134	1.26130703003	0.838553296489	4.27410988312	-1.03382280228	6.78361385523	0.0352965317934	-0.31735116634	0.127865319195	0.325153366579	0.0517851767563	-0.507345595405	-0.151037883668	0.601980928829	-0.110005814993	0.479060554762	0.0726625704522	-0.019843930918	0.382338836322	-0.0322181830388	0.326413819203	192.37883191	-8.98087295062	198.203684405
10	6.19541503641	1.11142015406	3.79373273869	4.41529672616	3.19329747466	8.11154759984	0.333018824318	-0.188706915678	-0.257291899175	0.251100329348	-0.0776143678892	-0.114587947672	0.416746608842	-0.402864584614	-0.314053619785	0.29576646696	0.0903034157049	0.0926789642057	0.441764479588	0.0999477063257	0.512938630933	196.004769277	-17.1155749633	174.410963402
11	6.85516196668	-3.0665400987	4.38134050406	7.77182232265	-2.67764716912	3.0070574174	0.0677752707245	0.829036527139	-0.739013696039	-0.630918666154	0.476754608888	-0.311325406887	-0.600074387902	-0.808356162185	-0.626053823519	0.51893173939	0.118397096786	0.132154833516	0.82652960725	-0.00724054018122	0.514280633289	193.817651573	-18.8837671166	160.05037386
12	6.08021389552	0.365172121978	0.0987526594223	0.744663032898	0.675468458868	3.62832691999	0.328717895637	0.418377473805	0.150788495544	0.0226664913811	-0.175585468735	-0.0613188794687	-0.252843221671	-0.109029714234	-0.152686034145	0.504039066	0.112132961358	0.143386920421	0.393939263396	0.0618008816093	0.427323755613	196.615327165	-12.5685492859	170.235623357
13	3.34483009434	-0.187554427338	-1.56080889371	3.01486179255	-0.803916002057	7.1028354792	0.273583051663	-0.286643096979	-0.155306978991	0.119060623079	-0.0741891202769	-0.292282547921	-0.115813300697	1.03799715041	-0.190283295787	0.370956146333	0.0964990833685	0.0532458837863	0.439820846305	-0.0888087644295	0.423358708468	201.061364619	-11.0571041985	183.737418921
14	5.92377469518	0.708018849133	0.581783130107	1.80341837692	-0.361000464392	4.800512759	-0.0619213459081	-0.546184903192	-0.361674552289	0.38350179655	0.0603983172305	-0.378390301839	-0.0113702580764	0.146572465584	-0.129155150401	0.551271448243	0.0627583591967	-0.0296975646933	0.337211503142	0.0563051148696	0.337714820199	186.958625237	-14.2936305295	200.757004585
15	3.38346858586	0.535725070331	-0.120298082606	4.62387353316	-1.04675414498	4.24400755833	-0.0362441273175	0.531300606502	0.0844653103569	-0.436137193343	-0.00682466297164	0.203598734788	0.0310516595076	-0.358471772519	-0.0134349468639	0.447194437147	0.0670478360487	0.0112872368702	0.33158416301	-0.00426374920881	0.279250130087	174.857695014	-7.72118122708	186.102588383
16	3.20322924423	-0.197101216588	-0.0289264657618	4.89692268779	0.0324388676258	4.37711800713	0.123454700152	-0.0104291634026	0.343250581911	-0.08155540156	-0.0279782667442	0.647115847183	-0.599966381582	-0.613477064786	-0.166483584648	0.493400108938	0.0764946770346	0.0532862697422	0.327708093531	0.00450093587144	0.397026697552	171.790873024	-0.619032752535	194.091967451
17	7.06227439521	-5.27396362883	-5.4624557735	5.8598031412	6.96591863177	8.58481905774	-0.0564803030965	-0.378827592142	0.447091433236	-0.0103408221056	0.375455756136	-0.674434801318	-0.328960594931	0.835022723348	-0.276324611107	0.537157864384	-0.0377773645036	0.0262094301189	0.284045450364	-0.00574577469336	0.42804168822	186.684059561	3.61537426391	198.904710279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 36 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 122 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 123 through 167 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 168 through 193 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 239 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 308 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 309 through 330 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 331 through 371 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 35 through 66 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 98 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 99 through 122 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 123 through 172 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 173 through 193 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 194 through 236 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 237 through 308 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 309 through 345 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 346 through 371 )

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