PDB-5twf: Regulation of protein interactions by MOB1 phosphorylation

ID or keywords:

Entry

Database: PDB / ID: 5twf

Title

Regulation of protein interactions by MOB1 phosphorylation

Components

MOB kinase activator 1A

Keywords

SIGNALING PROTEIN / non-phosphorylated / auto-inhibited / MOB1A

Function / homology

Function and homology information

hippo signaling / Signaling by Hippo / protein kinase activator activity / positive regulation of protein phosphorylation / extracellular exosome / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.136 Å

Authors

Xiong, S. / Sicheri, F.

Citation

Journal: Mol. Cell Proteomics / Year: 2017
Title: Regulation of Protein Interactions by Mps One Binder (MOB1) Phosphorylation.
Authors: Xiong, S. / Couzens, A.L. / Kean, M.J. / Mao, D.Y. / Guettler, S. / Kurinov, I. / Gingras, A.C. / Sicheri, F.

History

Deposition	Nov 13, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 19, 2017	Group: Database references
Revision 1.2	Jun 14, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5twf.cif.gz	164.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5twf.ent.gz	133.2 KB	Display	PDB format
PDBx/mmJSON format	5twf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5twf_validation.pdf.gz	442.8 KB	Display	wwPDB validaton report
Full document	5twf_full_validation.pdf.gz	452.6 KB	Display
Data in XML	5twf_validation.xml.gz	16.6 KB	Display
Data in CIF	5twf_validation.cif.gz	21.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/5twf ftp://data.pdbj.org/pub/pdb/validation_reports/tw/5twf	HTTPS FTP

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Related structure data

Related structure data	5twg 5twh
Similar structure data	3p2i-1 4hyn-2 3pb3-2 5ldo-2 2vyo-d 3p2k-3 1h2f-d 4ws8-d 3uyx-1 6ug4-3 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

5twg

5twh

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: MOB kinase activator 1A

B: MOB kinase activator 1A

hetero molecules

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

1

A: MOB kinase activator 1A

hetero molecules

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

2

B: MOB kinase activator 1A

hetero molecules

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

3

A: MOB kinase activator 1A

hetero molecules

A: MOB kinase activator 1A

hetero molecules

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

4

B: MOB kinase activator 1A

hetero molecules

B: MOB kinase activator 1A

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.132, 86.160, 138.081
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B Mass: 25112.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H8S9
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

#1: Protein

MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B

Mass: 25112.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9H8S9

#2: Chemical

ChemComp-ZN / ZINC ION

Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 52.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 5.5 / Details: 0.1 M MES pH 5.5, 0.2 M NH4Cl, and 20% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 3.1→30 Å / Num. obs: 9254 / % possible obs: 99.32 % / Redundancy: 3.5 % / Net I/σ(I): 13.5

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 3.136→25.4 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2911	443	4.79 %
R_work	0.2634	-	-
obs	0.2646	9254	99.32 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.136→25.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2954	0	2	0	2956

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3037
X-RAY DIFFRACTION	f_angle_d	1.269	4142
X-RAY DIFFRACTION	f_dihedral_angle_d	17.755	1766
X-RAY DIFFRACTION	f_chiral_restr	0.071	464
X-RAY DIFFRACTION	f_plane_restr	0.008	532

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 (%)
3.1358-3.5885	0.4124	154	0.3454	2884	X-RAY DIFFRACTION	98
3.5885-4.517	0.2921	135	0.2747	2899	X-RAY DIFFRACTION	100
4.517-25.4005	0.2428	154	0.2269	3028	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	3.5214	-0.4239	0.7185	3.7621	0.3638	3.5377	-0.2219	-0.3449	-0.1735	0.6237	0.2337	-0.0646	0.2882	-0.2406	0.0086	0.729	0.1299	0.0595	0.3888	0.0606	0.4271	12.6788	3.09	7.0539
2	7.7055	1.6781	2.036	1.8902	-2.4247	5.9185	-0.2222	-0.0717	0.5955	0.3376	-0.0797	0.2764	-0.8455	0.0018	0.2082	1.817	0.2148	0.1336	0.3726	1.0794	1.2954	16.805	26.0447	-10.6368
3	6.2572	3.6501	-3.8705	8.4013	2.819	6.498	0.3005	0.6171	0.4814	-0.3445	0.4412	0.9157	-0.4066	0.1677	-0.7354	1.8949	0.1973	-0.437	0.7132	-0.0656	1.16	14.2421	29.5304	2.9198
4	3.3396	-0.0566	-2.6852	1.2008	0.2434	2.4245	0.3124	-0.7307	0.1278	0.6674	0.6474	-0.1092	0.644	1.3083	-0.8347	2.2009	-0.0805	-0.4367	1.1306	-0.129	1.0759	24.4644	30.1012	7.7161
5	6.1153	4.8493	-2.8536	8.9892	-0.3535	3.4493	-0.1041	0.2206	0.7078	-0.6336	0.0922	0.9888	-0.1394	0.7924	-0.2533	1.058	0.016	-0.2547	0.5443	-0.0385	0.7492	23.3607	18.8499	3.735
6	3.0665	-3.7766	-0.2081	4.6812	0.2456	0.0366	-0.2799	-0.6785	0.0275	1.0775	0.4953	-0.3071	-0.4525	1.1294	0.0093	1.1694	0.0187	-0.4301	0.9439	-0.0543	0.6767	24.3443	7.0372	18.0724
7	3.2078	-1.4871	-1.3332	1.7182	0.4586	4.5796	-0.0332	-0.6286	1.4199	-0.4447	0.4328	-0.129	-0.8409	-0.0997	-0.1851	1.184	0.0957	-0.126	0.2105	0.1055	0.7909	12.3236	19.2386	5.0509
8	2.657	-2.3237	-1.1194	2.736	-0.5186	3.4937	-0.2483	1.3128	0.6276	-0.5316	0.3425	0.125	-0.6044	-1.1907	-0.1612	1.2172	-0.1575	-0.0896	0.9688	0.1694	0.7684	6.7835	16.9975	-11.4376
9	4.0213	0.803	-0.5752	4.9134	1.694	5.7182	-0.9526	-0.4794	1.0811	0.5544	0.6504	0.5394	-0.8036	-0.9142	0.1757	0.7709	0.3226	-0.179	0.4319	-0.1085	0.73	5.4034	13.6148	7.4211
10	2.9123	-3.1297	-1.1282	4.0143	2.6201	3.4051	0.2469	0.6917	0.412	-0.608	-0.2159	-0.1729	-0.3111	0.3936	-0.0988	0.5861	2.0015	-0.7223	0.939	0.2729	0.9446	-2.4316	18.2313	3.4978
11	3.2676	-0.7236	1.8207	6.5222	0.6808	3.3964	0.5865	-0.4144	0.0569	0.3164	-0.411	0.3272	0.1209	-0.5781	-0.0963	0.4503	-0.0516	0.0922	0.7196	0.0829	0.3017	3.1545	30.5506	41.5267
12	1.2622	-1.3565	-0.8056	3.9569	-0.44	1.1846	0.7496	-0.9529	0.7736	0.2446	-0.1057	-1.2105	-0.7282	1.911	-0.6152	0.9683	-0.1584	0.4842	2.1724	-0.2044	1.184	25.7618	26.2777	23.7929
13	2.0039	7.539	-1.5991	3.0347	-0.6413	0.142	-0.5229	-0.5243	-0.8909	-0.8304	-0.4565	-0.608	0.0226	-0.3434	1.0335	0.7851	-0.227	0.2918	1.9321	0.0312	0.873	30.3764	32.4955	35.2903
14	5.9534	1.5491	-1.758	8.5728	0.7013	4.2019	1.068	-0.6144	-0.6553	0.4038	-0.7302	-1.3917	0.9937	-0.4453	-0.3167	0.872	-0.0294	-0.0619	1.7286	0.377	1.1784	29.4175	19.7394	41.8409
15	8.3471	-4.2219	0.826	4.5683	1.7772	2.8566	0.6085	1.1194	0.1256	-0.1965	0.2511	-0.4363	0.9356	0.2393	-0.8624	0.5565	0.1427	-0.0509	0.8753	0.2325	0.9163	19.4196	20.022	38.0077
16	9.6277	5.323	-1.2991	3.789	-0.7605	0.9737	0.9062	-0.9054	-0.937	0.7821	-0.0927	-0.3843	0.8661	-0.1953	-0.677	1.1372	-0.2395	-0.124	0.9017	0.2234	0.5426	7.2594	18.5026	52.1987
17	3.2709	-0.4833	1.2588	3.5595	2.0221	7.7365	-0.0454	1.2276	0.4539	-0.3258	-0.2891	-0.4175	-0.5897	1.0511	0.0499	0.3762	-0.0345	0.0571	1.0292	0.1338	0.793	18.4274	32.7968	33.4839
18	8.3312	0.8448	-3.2496	4.0696	-0.9898	2.0088	0.3966	-0.2011	0.7011	0.0677	-0.7029	-0.0145	-1.7207	0.4748	0.3041	0.5935	0	-0.029	0.3661	0.1345	0.6008	10.1028	37.7465	39.3212
19	2.4101	-0.6454	-0.1102	0.1751	0.057	0.0227	0.2004	0.0302	0.4657	-0.044	-0.0774	-1.1297	-0.4625	0.8312	-0.088	0.783	-0.3742	-0.1686	0.8294	0.3102	1.406	19.4291	40.8126	43.0023

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 78 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 79 through 88 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 89 through 101 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 102 through 113 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 114 through 130 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 131 through 148 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 149 through 167 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 168 through 180 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 181 through 206 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 207 through 214 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 25 through 78 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 79 through 88 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 89 through 98 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 99 through 113 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 114 through 129 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 130 through 148 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 149 through 179 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 180 through 196 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 197 through 214 )

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