PDB-4v0v: The crystal structure of mouse PP1G in complex with truncated hum...

ID or keywords:

Entry

Database: PDB / ID: 4v0v

Title

The crystal structure of mouse PP1G in complex with truncated human PPP1R15B (631-660)

Components

PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

Keywords

HYDROLASE/HYDROLASE REGULATOR / HYDROLASE-HYDROLASE REGULATOR COMPLEX

Function / homology

Function and homology information

Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids ...
Similarity search - Function

Biological species

MUS MUSCULUS (house mouse)

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.61 Å

Authors

Chen, R. / Yan, Y. / Casado, A.C. / Ron, D. / Read, R.J.

Citation

Journal: Elife / Year: 2015
Title: G-actin provides substrate-specificity to eukaryotic initiation factor 2 alpha holophosphatases.
Authors: Chen, R. / Rato, C. / Yan, Y. / Crespillo-Casado, A. / Clarke, H.J. / Harding, H.P. / Marciniak, S.J. / Read, R.J. / Ron, D.

History

Deposition	Sep 18, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 27, 2019	Group: Data collection / Database references / Other Category: citation / pdbx_database_proc / pdbx_database_status Item: _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 1.2	Jan 10, 2024	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_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	4v0v.cif.gz	272.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4v0v_validation.pdf.gz	443.4 KB	Display	wwPDB validaton report
Full document	4v0v_full_validation.pdf.gz	445 KB	Display
Data in XML	4v0v_validation.xml.gz	27.2 KB	Display
Data in CIF	4v0v_validation.cif.gz	39.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/4v0v ftp://data.pdbj.org/pub/pdb/validation_reports/v0/4v0v	HTTPS FTP

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Related structure data

Related structure data	4v0uC 4v0wC 4v0xC 1fjmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4v0u-3 4v0w-1 4g9j-2 6czo-1 4v0u-1 5yqt-1 5zt0-2 4v0x-d 1pw1-d 1pwg-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	#176 - Aug 2014 Dynein similarity (6) #166 - Oct 2013 Proteasome similarity (1) #225 - Sep 2018 Phytase similarity (3)

Deposited unit

A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

hetero molecules

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

1

A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

hetero molecules

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

2

C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT

D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.800, 67.890, 156.380
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PROTEIN PHOSPHATASE 1C CATALYTIC SUBUNIT Mass: 33921.035 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-300 Source method: isolated from a genetically manipulated source Details: TRUNCATED MOUSE PP1G INCLUDING RESIDUES OF 7- 300 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21 (bacteria) References: UniProt: P63087, protein-serine/threonine phosphatase
#2: Protein/peptide	PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B Mass: 4059.541 Da / Num. of mol.: 2 / Fragment: RESIDUES 631-660 Source method: isolated from a genetically manipulated source Details: TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-660 Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5SWA1
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 422 / 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: 2.63 Å³/Da / Density % sol: 53.27 % / Description: NONE
Crystal grow	pH: 7 / Details: 2.4M SODIUM MALONATE, PH7.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 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: 1.61→51.26 Å / Num. obs: 92584 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 6.3 % / B_iso Wilson estimate: 17.56 Å² / R_merge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shell	Resolution: 1.61→1.65 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.81 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
CCP4I		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FJM

1fjm

Resolution: 1.61→51.263 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 19.09 / Stereochemistry target values: ML / Details: RESIDUE 22-26 IN CHAIN C ARE DISORDERED.

	R_factor	Num. reflection	% reflection
R_free	0.2029	4634	5 %
R_work	0.1763	-	-
obs	0.1776	92584	99.76 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.41 Å²

Refinement step

Cycle: LAST / Resolution: 1.61→51.263 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5017	0	4	422	5443

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5183
X-RAY DIFFRACTION	f_angle_d	1.044	7005
X-RAY DIFFRACTION	f_dihedral_angle_d	13.039	1945
X-RAY DIFFRACTION	f_chiral_restr	0.043	753
X-RAY DIFFRACTION	f_plane_restr	0.004	913

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 (%)
1.61-1.6283	0.2982	169	0.2634	2895	X-RAY DIFFRACTION	100
1.6283-1.6475	0.3065	164	0.2503	2880	X-RAY DIFFRACTION	100
1.6475-1.6676	0.2824	146	0.2399	2912	X-RAY DIFFRACTION	100
1.6676-1.6887	0.2519	163	0.2305	2868	X-RAY DIFFRACTION	100
1.6887-1.7109	0.2734	143	0.2236	2931	X-RAY DIFFRACTION	100
1.7109-1.7343	0.2251	145	0.2244	2908	X-RAY DIFFRACTION	100
1.7343-1.7591	0.256	161	0.2129	2924	X-RAY DIFFRACTION	100
1.7591-1.7854	0.2136	159	0.2009	2873	X-RAY DIFFRACTION	100
1.7854-1.8133	0.2627	148	0.1945	2901	X-RAY DIFFRACTION	100
1.8133-1.843	0.2219	151	0.1918	2916	X-RAY DIFFRACTION	100
1.843-1.8748	0.2261	184	0.1864	2875	X-RAY DIFFRACTION	100
1.8748-1.9089	0.2074	152	0.1804	2941	X-RAY DIFFRACTION	100
1.9089-1.9456	0.1955	143	0.1857	2905	X-RAY DIFFRACTION	100
1.9456-1.9853	0.2006	150	0.175	2919	X-RAY DIFFRACTION	100
1.9853-2.0285	0.1883	158	0.1735	2927	X-RAY DIFFRACTION	100
2.0285-2.0756	0.22	145	0.1694	2922	X-RAY DIFFRACTION	100
2.0756-2.1276	0.1924	162	0.1736	2895	X-RAY DIFFRACTION	100
2.1276-2.1851	0.2043	148	0.1679	2931	X-RAY DIFFRACTION	100
2.1851-2.2494	0.1995	161	0.1633	2906	X-RAY DIFFRACTION	100
2.2494-2.322	0.1998	163	0.1598	2931	X-RAY DIFFRACTION	100
2.322-2.405	0.1918	165	0.16	2920	X-RAY DIFFRACTION	100
2.405-2.5013	0.2059	153	0.1694	2933	X-RAY DIFFRACTION	100
2.5013-2.6151	0.207	149	0.187	2938	X-RAY DIFFRACTION	100
2.6151-2.753	0.2015	154	0.1779	2938	X-RAY DIFFRACTION	100
2.753-2.9254	0.1958	161	0.1792	2935	X-RAY DIFFRACTION	99
2.9254-3.1513	0.2185	145	0.1718	2977	X-RAY DIFFRACTION	100
3.1513-3.4683	0.1779	136	0.1608	2964	X-RAY DIFFRACTION	99
3.4683-3.97	0.1784	151	0.1542	3009	X-RAY DIFFRACTION	99
3.97-5.0012	0.1426	141	0.1505	3010	X-RAY DIFFRACTION	99
5.0012-51.289	0.2346	164	0.1948	3166	X-RAY DIFFRACTION	99

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	7.4517	2.213	1.1806	5.844	1.104	3.243	-0.2043	0.3602	0.3794	-0.4578	0.2209	-0.0878	-0.2199	0.3067	-0.0322	0.2391	0.0444	0.0654	0.2952	0.031	0.1709	-3.6451	-12.6787	-4.9424
2	1.8613	-0.0082	0.2238	1.9659	-0.1603	1.743	0.0476	0.1034	0.0436	-0.0127	-0.0077	-0.0433	-0.0559	0.1117	-0.036	0.0765	0.0041	0.0356	0.1274	-0.0279	0.0985	-7.9184	-20.738	6.797
3	0.8908	-0.3216	-0.232	1.1737	-0.0447	1.7396	0.0537	0.0417	0.076	0.0403	-0.0198	0.0903	-0.1981	-0.1402	-0.0368	0.0838	-0.0004	0.0177	0.1383	-0.0128	0.1239	-14.1903	-16.808	8.3093
4	1.8076	-0.0092	0.2745	1.7252	-0.1542	3.6094	-0.0115	-0.1113	-0.0147	0.0627	0.0767	0.202	0.1233	-0.3136	-0.0505	0.1372	0.0165	0.0292	0.1556	0.0251	0.1704	-19.8543	-24.2669	23.9139
5	3.1277	-2.4714	0.0429	5.7186	0.5523	2.3879	-0.1575	-0.2807	-0.0116	0.2618	0.1627	-0.0886	-0.0264	-0.0491	-0.0032	0.0923	-0.0123	0.0295	0.1331	0.0291	0.0742	-14.9588	-24.8432	32.4812
6	2.6061	0.3712	-0.709	4.1964	-2.0039	3.2326	-0.1104	-0.3013	-0.0779	0.1671	-0.0561	-0.3111	-0.0207	0.3296	0.1423	0.0963	0.008	0.0001	0.1835	-0.0149	0.128	-2.8189	-23.2841	25.1839
7	2.6591	1.4445	-0.1648	1.217	-0.8109	1.8437	0.0125	-0.036	0.325	-0.1111	-0.0441	-0.3246	-0.215	0.1852	0.038	0.1581	-0.0217	0.011	0.231	-0.016	0.2365	3.5714	-20.2787	18.1027
8	3.7198	-0.7507	0.1636	3.7102	-0.5705	1.9851	0.0665	-0.6194	0.2306	1.0012	0.0895	-0.3971	-0.2128	0.2903	-0.1575	0.5603	-0.0144	-0.0578	0.3171	-0.075	0.2138	-29.6452	9.1145	46.441
9	4.0616	0.9444	1.5441	2.7412	0.7112	4.1534	0.3099	-0.3903	-0.4701	0.6724	-0.0923	-0.1815	0.5879	0.0154	-0.0372	0.3704	-0.0162	-0.0013	0.1337	0.0256	0.1445	-35.5091	-3.6707	40.1714
10	2.1033	0.0143	-0.1539	2.3241	0.4126	2.3888	0.1193	0.0091	0.0956	0.0876	-0.0087	-0.0928	-0.1424	0.057	-0.0677	0.1501	-0.0158	0.0197	0.0924	-0.0092	0.0905	-35.883	11.3477	30.3011
11	1.8484	-0.1869	-0.2537	1.9751	0.4168	2.7354	0.0048	-0.0744	-0.0636	0.1685	-0.0037	-0.0585	0.0859	0.0497	-0.0378	0.1209	-0.0108	-0.0002	0.0629	0.0008	0.0898	-35.4796	4.4787	33.6261
12	3.4411	0.0499	0.4151	2.9518	0.0138	7.6981	0.0536	-0.2285	0.0609	0.1857	-0.0357	-0.4937	0.1719	0.4731	-0.0316	0.1792	0.0503	-0.0372	0.1738	-0.0221	0.2223	-19.6117	-1.5977	31.6524
13	4.2865	-1.7663	2.0585	2.6252	-0.8739	3.7272	0.0347	-0.1412	-0.1683	0.1161	0.073	0.0103	0.3054	-0.0895	-0.1353	0.123	-0.0142	0.0233	0.0768	-0.0193	0.097	-36.9653	-0.9399	28.0182
14	1.4188	0.8699	0.0187	2.5441	-1.0665	3.2369	-0.0179	0.1434	-0.2326	-0.2043	0.0445	0.0588	0.6165	-0.1497	-0.0131	0.2563	-0.0227	-0.0018	0.1714	-0.0288	0.1917	-41.0808	-6.6506	17.7848
15	2.6576	-1.0457	1.2946	3.4117	-0.1768	3.9515	-0.0115	0.1285	0.1421	-0.4377	-0.0199	-0.2224	0.0207	0.055	0.0169	0.1448	-0.0109	0.008	0.1336	-0.022	0.1404	-34.6627	2.0812	9.6558
16	3.5999	-1.7663	0.0082	3.7146	0.0635	3.1583	0.0991	0.1544	-0.0996	-0.3162	-0.1151	0.0206	0.0449	-0.0726	0.0188	0.1412	-0.0151	-0.0035	0.0952	-0.0136	0.1031	-39.5288	2.4477	6.905
17	3.0122	-0.3525	1.5487	2.3363	0.2031	3.4368	-0.0272	0.1402	0.2869	-0.2311	-0.0524	-0.0703	-0.414	0.0675	0.0767	0.1582	-0.0057	0.0264	0.0912	0.0011	0.1292	-37.4779	13.9574	14.7409
18	1.3405	1.1286	1.0822	2.9696	0.1859	2.9805	-0.0363	0.0499	-0.0372	-0.1192	0.03	-0.2861	-0.1825	0.1798	-0.0312	0.213	-0.0055	0.0384	0.1096	-0.0167	0.1921	-34.3677	19.4978	22.4041
19	3.3707	2.7526	3.2225	3.416	1.8466	3.978	-0.3778	0.166	0.8752	-0.2685	-0.0486	0.3172	-0.6398	-0.0409	0.3043	0.3287	0.0114	0.0156	0.1734	-0.0089	0.2651	-40.5623	24.3288	20.8844
20	4.8818	1.5291	-0.8406	8.1978	-1.8848	6.143	-0.0435	-0.4843	-0.4624	0.0657	-0.1198	-1.0036	0.3047	0.6839	0.1301	0.1795	0.0472	0.0454	0.3312	0.0386	0.3555	6.0353	-33.2356	22.2774
21	6.024	0.5071	1.0397	4.4069	-0.1501	6.445	-0.3815	-0.128	0.3779	-0.0006	-0.0619	0.0144	-1.1447	0.3909	0.4154	0.5205	-0.1773	0.0848	0.4587	-0.0466	0.5062	9.0075	-10.1543	14.7416

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 6 THROUGH 31 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 32 THROUGH 99 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 100 THROUGH 172 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 173 THROUGH 215 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 216 THROUGH 239 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 240 THROUGH 271 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 272 THROUGH 300 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 6 THROUGH 31 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 32 THROUGH 48 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 49 THROUGH 99 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 100 THROUGH 127 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 128 THROUGH 145 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 146 THROUGH 172 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 173 THROUGH 199 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 200 THROUGH 215 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 216 THROUGH 239 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 240 THROUGH 271 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 272 THROUGH 300 )
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESID 639 THROUGH 653 )
20	X-RAY DIFFRACTION	20	CHAIN 'B' AND (RESID 639 THROUGH 648 )
21	X-RAY DIFFRACTION	21	CHAIN 'B' AND (RESID 649 THROUGH 658 )

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