PDB-3gni: Structure of STRAD and MO25

ID or keywords:

Entry

Database: PDB / ID: 3gni

Title

Structure of STRAD and MO25

Components

Protein Mo25
STRAD alpha

Keywords

SIGNALING PROTEIN/SIGNALING PROTEIN / kinase fold /

pseudokinase / alpha helical repeat protein / adaptor protein / ATP-binding /

Cell cycle /

Kinase / Nucleotide-binding /

Nucleus /

Phosphoprotein /

Transferase / METAL BINDING PROTEIN-TRANSFERASE COMPLEX /

SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX

Function / homology

Function and homology information

intracellular protein-containing complex / negative regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transport /

serine/threonine protein kinase complex / cellular hypotonic response / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / G1 to G0 transition / protein kinase activator activity / activation of protein kinase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Zeqiraj, E. / Goldie, S. / Alessi, D.R. / van Aalten, D.M.F.

Citation

Journal: Plos Biol. / Year: 2009
Title: ATP and MO25alpha regulate the conformational state of the STRADalpha pseudokinase and activation of the LKB1 tumour suppressor
Authors: Zeqiraj, E. / Filippi, B.M. / Goldie, S. / Navratilova, I. / Boudeau, J. / Deak, M. / Alessi, D.R. / van Aalten, D.M.

History

Deposition	Mar 17, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 16, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Download

PDBx/mmCIF format	3gni.cif.gz	148.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3gni.ent.gz	113.8 KB	Display	PDB format
PDBx/mmJSON format	3gni.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/gn/3gni ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gni	HTTPS FTP

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Related structure data

Related structure data	1u5rS 1upkS 1upl S: Starting model for refinement
Similar structure data	2vl8-2 4dmw-d 5rlt-2 2vkd-3 5rmk-2 5rlu-2 5rl6-2 4n0t-d 5rmg-2 5rl8-1 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

Deposited unit

A: Protein Mo25

B: STRAD alpha

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	73.678, 82.874, 134.292
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Protein Mo25 / Calcium-binding protein 39 Mass: 39922.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CAB39, MO25, CGI-66 / Plasmid: pOPC / Cell (production host): BL21(DE3)pLysS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y376
#2: Protein	STRAD alpha / STE20-related kinase adapter protein alpha / STE20-related adapter protein / Serologically defined ...STE20-related kinase adapter protein alpha / STE20-related adapter protein / Serologically defined breast cancer antigen NY-BR-96 Mass: 43762.617 Da / Num. of mol.: 1 / Fragment: Protein kinase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STRADA, LYK5, STRAD / Plasmid: pOPC / Cell (production host): BL21(DE3)pLysS / Production host: Escherichia coli (E. coli) / References: UniProt: Q7RTN6
#3: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.79 %
Crystal grow	Temperature: 293 K / pH: 6.4 Details: 0.1 M MES pH 6.4, 10% PEG8000, 0.25 microL of 1 M NDSB-256, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 15, 2007
Radiation	Monochromator: HORIZONTALLY DIFFRACTING SI (111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.873 Å / Relative weight: 1
Reflection	Resolution: 2.35→20 Å / Num. obs: 34668 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 5.5 % / R_merge(I) obs: 0.01 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.35→2.48 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.617 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
DNA		data collection
MOLREP		phasing
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1UPK AND 1U5R

1upk

1u5r

Resolution: 2.35→19.82 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.917 / SU B: 18.778 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.321 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.254	902	2.6 %	RANDOM
R_work	0.206	-	-	-
obs	0.207	33712	99.5 %	-

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: 28.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.93 Å²	0 Å²	0 Å²
2-	-	-0.28 Å²	0 Å²
3-	-	-	-2.64 Å²

Refinement step

Cycle: LAST / Resolution: 2.35→19.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5202	0	44	77	5323

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	5364
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	1.967	7251
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.942	5	633
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.767	24.402	259
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.585	15	965
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.295	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	800
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4009
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.196	0.2	2217
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.298	0.2	3643
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.12	0.2	171
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	0.191	0.2	73
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.207	0.2	3
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	1.063	1.5	3296
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.685	2	5168
X-RAY DIFFRACTION	r_scbond_it	3.042	3	2343
X-RAY DIFFRACTION	r_scangle_it	4.452	4.5	2083
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.35→2.413 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.374	61	-
R_work	0.256	2314	-
obs	-	4988	95.57 %

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	9.4971	-2.4993	33.374	0.6788	-8.8839	117.7653	0.1957	0.9983	-0.1654	0.3514	-0.6873	-0.7869	0.2148	2.8933	0.4916	0.1893	0.0108	-0.0778	0.218	0.0254	0.4465	9.0983	17.9254	-17.5156
2	13.1125	-2.5829	0.984	4.4585	-2.8308	4.9357	-0.1201	0.4179	0.3863	0.1968	0.037	-0.0484	-0.553	0.1942	0.0831	0.2073	-0.1164	-0.0121	-0.0349	0.0116	0.0451	0.0855	11.9948	-9.885
3	4.7337	-0.6983	1.8483	4.6765	-0.8076	6.1673	-0.2305	-0.0433	0.2051	0.0079	-0.0134	-0.6901	-0.3397	0.9287	0.2439	0.1344	-0.1208	0.0181	0.1047	-0.0052	0.132	9.0704	5.2438	-5.0367
4	5.8232	-0.3164	3.283	5.1488	-0.0865	7.6274	-0.1959	-0.0699	0.117	0.2311	0.0726	-0.444	-0.5188	0.5438	0.1233	0.06	-0.0404	0.001	0.0182	0.0034	0.0065	6.3465	-4.4418	3.6649
5	3.0698	0.4358	2.1311	3.5577	1.8296	9.3783	-0.1203	-0.1053	-0.0993	-0.0058	0.1157	0.2471	-0.4311	-0.1683	0.0046	-0.0456	-0.0071	0.0307	-0.0123	0.0629	0.0227	-0.8213	-16.9612	2.2626
6	17.4089	5.9454	-5.4651	8.788	-5.0365	4.6312	0.1894	-0.9648	-0.238	0.9583	-0.0685	-0.192	0.1131	0.5886	-0.1209	0.1158	0.0746	-0.0724	0.107	-0.0082	0.0049	9.8747	-19.4064	12.8491
7	2.9112	-1.2118	0.8813	5.423	0.7706	10.0953	-0.0393	0.0605	-0.2224	0.1358	-0.12	0.4614	0.1021	-0.1805	0.1593	-0.0768	-0.0325	0.0422	-0.0224	0.0647	0.1224	-0.6457	-28.1826	4.4044
8	1.6831	-0.5708	1.4491	6.1642	-0.6066	4.0993	-0.061	-0.1179	-0.1601	0.4256	0.0758	0.2827	0.3013	-0.0371	-0.0148	-0.0003	0.0706	0.0802	0.0498	0.1127	0.1729	3.1013	-36.7343	7.4036
9	4.2123	-0.1847	-0.4661	7.5457	-2.7292	9.8658	0.1497	-0.0951	-0.3289	0.0627	0.1169	0.2328	0.3774	0.2526	-0.2667	-0.0228	0.0625	-0.0117	0.0038	0.0781	0.2029	6.3084	-46.2143	5.6517
10	10.2824	1.4896	-6.7556	9.3105	-7.7979	15.1217	-0.1162	-0.6223	-0.5824	0.0643	0.022	0.2003	0.9878	0.3755	0.0942	0.0863	0.055	-0.0833	0.0756	0.0535	0.2892	12.2026	-50.3174	7.5462
11	24.0853	19.3876	12.0092	24.3759	1.7078	13.2112	0.4429	0.1579	-0.3497	0.2402	-0.037	-0.1623	0.389	-0.7376	-0.406	0.0909	0.1544	0.1932	0.166	0.0179	0.2904	-13.9458	3.5366	-3.4728
12	8.0679	-1.5235	-5.2293	6.0916	3.4712	11.158	0.0943	0.8474	-0.3772	-0.4203	-0.3744	0.5286	-0.0451	-1.5653	0.28	0.0465	-0.0139	-0.0576	0.1982	-0.0691	0.079	-8.6413	-23.2075	-24.3158
13	0.3336	1.6072	-1.4631	9.497	-5.4324	7.9088	0.0338	-0.2813	-0.0605	-0.3998	-0.1354	-0.0299	-0.1498	0.2116	0.1015	-0.0082	-0.0025	-0.0209	0.0847	-0.008	0.186	4.2435	-18.2881	-17.299
14	2.269	1.228	-4.7457	1.1369	-1.1899	19.5662	0.0408	0.1542	-0.0148	-0.3767	0.0233	0.17	-0.1935	-0.4011	-0.0641	-0.0061	0.0864	-0.09	0.0674	-0.0571	0.0676	-2.2771	-20.672	-30.0454
15	3.8003	0.7212	0.5302	4.3157	0.2492	6.0024	0.2179	-0.1231	0.3061	-0.3909	-0.2428	0.1702	-0.8166	0.1451	0.0249	0.2051	-0.0077	0.0397	0.0562	-0.0546	0.0304	7.2589	-10.0117	-31.0593
16	4.7235	-2.0436	0.2482	19.3518	5.2433	7.187	-0.1012	-0.0585	0.053	0.0972	0.3207	-0.4192	-0.3176	0.5739	-0.2195	0.2619	-0.1345	-0.016	0.7152	0.0332	0.2105	19.355	-14.7019	-17.701
17	4.1976	0.6756	1.7933	6.1304	3.1666	5.2262	0.3516	0.035	-0.2458	0.3522	0.0234	-0.6542	0.1501	1.2053	-0.375	0.1149	-0.0646	0.023	0.4086	0.0197	0.1527	20.1664	-16.0078	-31.9448
18	9.1112	-7.3237	2.788	14.4438	0.9546	8.252	0.0928	-0.0681	-1.0283	-0.36	0.7688	-0.2619	-0.2113	0.9245	-0.8616	0.3431	-0.1703	0.0812	0.523	-0.08	0.3297	22.034	-16.4202	-40.6211
19	1.5069	0.2015	-1.1342	2.497	-1.9974	5.9131	0.2037	0.2136	0.1615	-0.4901	0.0248	0.1647	-0.7008	0.0436	-0.2285	0.2009	0.0344	-0.011	0.0784	-0.1564	0.1287	7.4469	-14.1333	-32.1989
20	18.4068	10.2138	17.3011	11.0167	12.8957	29.0001	0.4358	-0.153	-0.9715	0.1821	-0.0722	-0.8722	0.999	0.7446	-0.3635	-0.0237	0.024	-0.0553	0.0432	0.1477	0.0527	6.5264	-19.1962	-21.6787
21	0.6127	-0.2711	0.1011	0.5274	0.4859	0.7079	-0.0466	-0.0889	-0.0384	-0.068	0.0367	0.0321	-0.1289	0.1204	0.0099	-0.0089	0.0105	0.0142	0.0617	0.0231	0.0713	3.506	-14.3895	-8.4316

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 14
2	X-RAY DIFFRACTION	2	A	15 - 57
3	X-RAY DIFFRACTION	3	A	58 - 107
4	X-RAY DIFFRACTION	4	A	108 - 159
5	X-RAY DIFFRACTION	5	A	160 - 192
6	X-RAY DIFFRACTION	6	A	193 - 205
7	X-RAY DIFFRACTION	7	A	206 - 237
8	X-RAY DIFFRACTION	8	A	238 - 271
9	X-RAY DIFFRACTION	9	A	272 - 316
10	X-RAY DIFFRACTION	10	A	317 - 336
11	X-RAY DIFFRACTION	11	B	-15 - -2
12	X-RAY DIFFRACTION	12	B	60 - 102
13	X-RAY DIFFRACTION	13	B	103 - 132
14	X-RAY DIFFRACTION	14	B	133 - 166
15	X-RAY DIFFRACTION	15	B	167 - 219
16	X-RAY DIFFRACTION	16	B	220 - 240
17	X-RAY DIFFRACTION	17	B	241 - 278
18	X-RAY DIFFRACTION	18	B	279 - 356
19	X-RAY DIFFRACTION	19	B	357 - 431
20	X-RAY DIFFRACTION	20	A	342
21	X-RAY DIFFRACTION	20	B	1
22	X-RAY DIFFRACTION	21	A	343 - 419

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