PDB-6ar2: Structure of human SLMAP FHA domain in complex with pMST2

ID or keywords:

Entry

Database: PDB / ID: 6ar2

Title

Structure of human SLMAP FHA domain in complex with pMST2

Components

ASP-GLY-TPO-MET-LYS-ARG
Sarcolemmal membrane-associated protein

Keywords

MEMBRANE PROTEIN / Hippo / SLMAP / FHA / phospho-MST2

Function / homology

Function and homology information

regulation of membrane depolarization during cardiac muscle cell action potential / negative regulation of cell growth involved in contact inhibition / protein localization to centrosome / positive regulation of hippo signaling / FAR/SIN/STRIPAK complex / hippo signaling / regulation of sodium ion transmembrane transport / transcription regulator activator activity / Signaling by Hippo / M band ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Osinski, A. / Ni, L. / Luo, X.

Funding support

United States, 2items

Citation

Journal: Elife / Year: 2017
Title: SAV1 promotes Hippo kinase activation through antagonizing the PP2A phosphatase STRIPAK.
Authors: Bae, S.J. / Ni, L. / Osinski, A. / Tomchick, D.R. / Brautigam, C.A. / Luo, X.

History

Deposition	Aug 21, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6ar2.cif.gz	177.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6ar2.ent.gz	144.6 KB	Display	PDB format
PDBx/mmJSON format	6ar2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ar/6ar2 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/6ar2	HTTPS FTP

-
Related structure data

Related structure data	6ao5C 6ar0SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6pwt-d 2vil-d 6ghv-1 3p6e-d 5o4y-1 6ghv-6 4cdl-d 3p6f-d 5oo9-d 6jzw-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (2) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #231 - Mar 2019 Measles Virus Proteins similarity (2) #56 - Aug 2004 Caspases similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Sarcolemmal membrane-associated protein

B: Sarcolemmal membrane-associated protein

C: ASP-GLY-TPO-MET-LYS-ARG

D: ASP-GLY-TPO-MET-LYS-ARG

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

1

A: Sarcolemmal membrane-associated protein

C: ASP-GLY-TPO-MET-LYS-ARG

defined by author&software
Evidence: gel filtration
17.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Sarcolemmal membrane-associated protein

D: ASP-GLY-TPO-MET-LYS-ARG

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

Unit cell

Length a, b, c (Å)	38.758, 70.534, 91.015
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Sarcolemmal membrane-associated protein / Sarcolemmal-associated protein Mass: 15789.931 Da / Num. of mol.: 2 / Fragment: UNP residues 1-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLMAP, KIAA1601, SLAP, UNQ1847/PRO3577 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14BN4
#2: Protein/peptide	ASP-GLY-TPO-MET-LYS-ARG Mass: 1290.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13188*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.82 Å³/Da / Density % sol: 32.45 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM KSCN, 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.55→38.24 Å / Num. obs: 36933 / % possible obs: 99.8 % / Redundancy: 12.5 % / R_pim(I) all: 0.029 / Net I/σ(I): 39.4
Reflection shell	Resolution: 1.55→1.59 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2719 / R_pim(I) all: 0.318 / % possible all: 97.3

-
Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6AR0

6ar0

Resolution: 1.55→38.239 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.62

	R_factor	Num. reflection	% reflection
R_free	0.1877	1846	5 %
R_work	0.1614	-	-
obs	0.1627	36924	99.74 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.55→38.239 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2210	0	0	203	2413

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2256
X-RAY DIFFRACTION	f_angle_d	1.005	3046
X-RAY DIFFRACTION	f_dihedral_angle_d	16.828	1366
X-RAY DIFFRACTION	f_chiral_restr	0.063	334
X-RAY DIFFRACTION	f_plane_restr	0.007	396

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 (%)
1.55-1.5919	0.3028	136	0.2748	2583	X-RAY DIFFRACTION	97
1.5919-1.6387	0.3196	140	0.2312	2660	X-RAY DIFFRACTION	100
1.6387-1.6916	0.2636	141	0.2055	2669	X-RAY DIFFRACTION	100
1.6916-1.7521	0.2314	140	0.1831	2652	X-RAY DIFFRACTION	100
1.7521-1.8222	0.2451	138	0.174	2665	X-RAY DIFFRACTION	100
1.8222-1.9052	0.2545	142	0.166	2685	X-RAY DIFFRACTION	100
1.9052-2.0056	0.192	140	0.1586	2676	X-RAY DIFFRACTION	100
2.0056-2.1312	0.1745	143	0.1499	2700	X-RAY DIFFRACTION	100
2.1312-2.2958	0.1955	142	0.1506	2704	X-RAY DIFFRACTION	100
2.2958-2.5268	0.18	143	0.1601	2701	X-RAY DIFFRACTION	100
2.5268-2.8923	0.2034	143	0.1614	2730	X-RAY DIFFRACTION	100
2.8923-3.6435	0.175	145	0.1513	2758	X-RAY DIFFRACTION	100
3.6435-38.251	0.1605	153	0.1577	2895	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	3.5618	-1.5821	-0.4493	3.2968	0.1514	2.9911	-0.0412	-0.2715	0.0105	0.2886	-0.1133	0.1485	-0.1748	0.0652	0.1559	0.2377	-0.0492	0.0305	0.276	-0.0314	0.2506	7.8517	156.6078	120.0852
2	4.482	-1.7329	-0.3457	3.7433	0.4716	5.6748	0.2439	-0.2033	-0.0675	0.0035	-0.0341	-0.0316	0.5124	0.312	-0.1142	0.2406	-0.0094	0.0097	0.2413	0.015	0.2349	9.9693	146.493	114.7527
3	7.3961	-2.7873	4.7731	3.9101	-3.8165	6.3637	0.2226	-0.4128	-0.4118	-0.0475	0.0727	0.4352	0.2321	-0.5714	-0.2284	0.2446	-0.0231	0.0088	0.3218	-0.0035	0.2858	-1.9086	150.1394	114.3928
4	4.3171	-0.6129	1.4721	1.1407	0.4476	2.0835	0.1282	0.1612	-0.205	-0.0241	-0.0597	0.0044	0.0806	0.1843	-0.09	0.1777	0.0069	0.0125	0.1937	-0.0035	0.1975	13.3758	150.6264	106.7184
5	3.2902	0.4073	1.2703	1.9357	0.1089	3.1335	-0.0411	0.2133	0.3971	-0.1595	-0.0617	0.1383	-0.2831	0.0691	0.1001	0.2458	-0.0068	-0.0072	0.2344	0.0106	0.255	7.795	160.8095	105.2739
6	7.7372	2.0822	1.629	0.6644	0.7018	1.073	-0.3835	0.1099	1.1302	-0.1848	-0.0087	0.1078	-0.2086	-0.33	0.2614	0.3947	0.0312	-0.075	0.4841	-0.0974	0.5871	-11.2799	166.5626	110.9897
7	5.3726	-3.1052	0.9685	2.1795	-0.3132	0.329	-0.0755	-0.0327	-0.1073	0.1302	-0.0876	0.019	-0.1446	0.0883	0.1791	0.222	-0.0414	0.0002	0.2765	0.0153	0.2586	12.7543	157.3242	117.7616
8	3.9193	-1.8331	-1.4306	2.0078	0.5907	4.2297	0.3659	-0.2744	-0.0246	1.0126	-0.404	-1.4074	0.0271	1.1644	0.1831	0.3621	0.0018	-0.0686	0.6201	0.0694	0.418	24.4685	149.9259	119.4139
9	5.1056	0.8188	-4.5934	3.3603	-1.1674	8.612	-0.2352	-0.1066	-0.4519	-0.3606	0.1639	0.0246	0.4571	0.0059	-0.0794	0.2951	0.0182	-0.0021	0.2155	0.0312	0.2323	-4.8176	129.7071	91.4299
10	4.2931	0.4513	-1.1982	5.2791	-0.675	3.2039	0.0136	-0.5533	-0.2021	0.1248	-0.029	0.4671	0.0369	0.19	0.0221	0.1963	0.0425	0.0178	0.2398	0.0553	0.2326	-7.5861	134.6214	101.61
11	2.2939	1.6271	2.839	1.9781	2.0939	3.5382	0.6115	-0.9586	-0.6059	1.2527	-0.5021	-0.4847	-0.0178	1.1742	-0.3164	0.3533	0.0226	-0.0681	0.5589	0.0747	0.336	7.6288	135.7403	101.1036
12	2.4833	0.13	-0.9479	1.7728	0.4608	1.9824	-0.1191	-0.3996	-0.1194	-0.0735	0.1579	-0.1134	0.1306	0.4329	-0.0235	0.2283	0.0289	0.0012	0.2941	-0.0078	0.2008	-1.6572	138.7183	96.8907
13	3.4789	-0.1454	-0.7139	1.503	0.4161	1.5551	-0.0224	0.2199	0.1011	-0.2782	0.0856	0.0208	-0.1952	-0.0071	-0.0625	0.2763	-0.0238	-0.0149	0.2423	0.0071	0.2185	-7.6966	144.257	90.0839
14	3.1817	-0.7826	1.7014	1.7779	0.5641	2.193	0.0204	0.4292	0.2195	0.1062	0.2379	-0.3382	-0.2878	0.5796	-0.1972	0.333	-0.0765	0.0535	0.5514	-0.1652	0.4458	14.0947	139.8658	81.6351
15	9.4562	2.4833	-6.9783	0.7709	-2.0011	5.4059	-0.3017	0.1892	-0.1298	-0.3862	0.2434	0.145	0.2318	0.0124	0.112	0.3508	-0.0396	0.0017	0.215	0.027	0.322	-9.8394	131.9037	90.4452
16	4.2293	0.5106	-0.1267	5.3595	-0.5724	1.9527	-0.2057	0.3354	-0.8337	0.1379	0.0964	1.5028	0.7948	-1.8899	0.2797	0.3751	-0.0552	0.0918	0.4345	0.0042	0.7262	-21.6337	129.4256	97.589
17	5.705	3.0204	0.5259	9.6058	0.6019	4.8334	-0.6487	0.0617	1.16	0.3925	0.3796	0.9225	-0.3464	-0.3131	0.302	0.2505	0.0306	-0.0772	0.3144	-0.0408	0.4127	-5.9234	159.071	103.7407
18	7.1215	-0.9285	-1.9058	8.7102	1.6004	6.5018	0.2135	0.512	0.3749	-0.7505	0.1145	-0.8182	-0.3454	1.2091	-0.3574	0.3795	-0.0988	0.0805	0.5598	-0.0496	0.4311	8.8609	146.7336	89.9029

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 19 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 20 through 30 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 50 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 51 through 71 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 72 through 111 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 112 through 120 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 121 through 128 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 129 through 135 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 19 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 20 through 30 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 31 through 40 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 41 through 61 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 62 through 111 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 112 through 120 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 121 through 128 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 129 through 135 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 376 through 381 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 376 through 381 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi