PDB-7d2s: Crystal structure of Rsu1/PINCH1_LIM5C complex

ID or keywords:

Entry

Database: PDB / ID: 7d2s

Title

Crystal structure of Rsu1/PINCH1_LIM5C complex

Components

LIM and senescent cell antigen-like-containing domain protein 1
Ras suppressor protein 1

Keywords

PROTEIN BINDING / Leucine Rich Repeat

Function / homology

Function and homology information

Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of integrin-mediated signaling pathway / Cell-extracellular matrix interactions / cell-cell junction organization / positive regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of GTPase activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.653 Å

Authors

Yang, H. / Wei, Z. / Cong, Y.

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	31870757	China
National Natural Science Foundation of China (NSFC)	31971131	China
National Natural Science Foundation of China (NSFC)	31770791	China

Citation

Journal: Elife / Year: 2021
Title: Complex structures of Rsu1 and PINCH1 reveal a regulatory mechanism of the ILK/PINCH/Parvin complex for F-actin dynamics.
Authors: Yang, H. / Lin, L. / Sun, K. / Zhang, T. / Chen, W. / Li, L. / Xie, Y. / Wu, C. / Wei, Z. / Yu, C.

History

Deposition	Sep 17, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7d2s.cif.gz	133.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d2/7d2s ftp://data.pdbj.org/pub/pdb/validation_reports/d2/7d2s	HTTPS FTP

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Related structure data

Related structure data	7d2tC 7d2uC 4u06S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2y9h-7 3vc1-2 3vc1-6 1rhc-d 3vc2-7 1uw5-2 3juu-2 4fjo-3 3qm1-d 4gx9-1 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
Related items in Molecule of the Month	#143 - Nov 2011 Toll-like Receptors similarity (5) #248 - Aug 2020 Phytosulfokine Receptor similarity (5) #68 - Aug 2005 Neurotrophins similarity (2) #105 - Sep 2008 Ribonuclease A similarity (2) #245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: Ras suppressor protein 1

B: LIM and senescent cell antigen-like-containing domain protein 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	124.596, 124.596, 50.518
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

#1: Protein	Ras suppressor protein 1 / Rsu-1 Mass: 24699.371 Da / Num. of mol.: 1 / Fragment: UNP residues 1-215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RSU1, RSP1 / Plasmid: pFastbac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15404
#2: Protein	LIM and senescent cell antigen-like-containing domain protein 1 / Particularly interesting new Cys-His protein 1 / PINCH-1 / Renal carcinoma antigen NY-REN-48 Mass: 9148.917 Da / Num. of mol.: 1 / Fragment: UNP residues 249-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1, PINCH, PINCH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48059
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.9 Å³/Da / Density % sol: 57.53 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bicine pH8.5, 20% w/v PEG10000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 46579 / % possible obs: 100 % / Redundancy: 13.4 % / B_iso Wilson estimate: 23.82 Å² / R_merge(I) obs: 0.089 / R_pim(I) all: 0.025 / R_rim(I) all: 0.093 / Χ²: 1.052 / Net I/σ(I): 6.9 / Num. measured all: 623057

Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²
1.65-1.68	12.9	0.931	2321	0.823	0.269	0.969	0.763
1.68-1.71	13.6	0.795	2291	0.864	0.223	0.826	0.773
1.71-1.74	13.6	0.693	2349	0.9	0.194	0.72	0.784
1.74-1.78	13.5	0.589	2291	0.924	0.166	0.612	0.805
1.78-1.82	13.4	0.486	2315	0.947	0.137	0.505	0.83
1.82-1.86	13.1	0.385	2313	0.961	0.11	0.4	0.879
1.86-1.9	12.6	0.328	2311	0.967	0.096	0.342	0.938
1.9-1.96	13.3	0.265	2314	0.981	0.075	0.276	1
1.96-2.01	13.9	0.219	2335	0.987	0.061	0.227	1.106
2.01-2.08	13.8	0.188	2336	0.99	0.053	0.195	1.202
2.08-2.15	13.5	0.163	2283	0.993	0.046	0.169	1.227
2.15-2.24	13	0.144	2331	0.994	0.042	0.15	1.28
2.24-2.34	12.7	0.124	2315	0.994	0.036	0.129	1.377
2.34-2.46	13.9	0.109	2340	0.996	0.03	0.113	1.429
2.46-2.62	13.8	0.1	2323	0.996	0.028	0.103	1.331
2.62-2.82	13.6	0.09	2328	0.995	0.025	0.093	1.214
2.82-3.11	12.9	0.082	2340	0.997	0.024	0.085	1.079
3.11-3.55	14.1	0.073	2348	0.998	0.02	0.076	1.056
3.55-4.48	13	0.064	2379	0.998	0.018	0.066	0.978
4.48-50	13.3	0.063	2416	0.997	0.018	0.066	0.968

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.9_1692	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U06

4u06

Resolution: 1.653→50 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1845	2355	5.06 %
R_work	0.166	44215	-
obs	0.1669	46570	99.8 %

Solvent computation

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

Displacement parameters

B_iso max: 93.11 Å² / B_iso mean: 32.8943 Å² / B_iso min: 15.7 Å²

Refinement step

Cycle: final / Resolution: 1.653→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2175	0	14	187	2376
B_iso mean	-	-	32.17	38.82	-
Num. residues	-	-	-	-	276

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2293
X-RAY DIFFRACTION	f_angle_d	1.012	3115
X-RAY DIFFRACTION	f_chiral_restr	0.042	367
X-RAY DIFFRACTION	f_plane_restr	0.005	401
X-RAY DIFFRACTION	f_dihedral_angle_d	12.833	899

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.653-1.6863	0.2714	134	0.2411	2561	97
1.6863-1.7229	0.2443	143	0.2173	2546	100
1.7229-1.763	0.2171	139	0.2153	2606	100
1.763-1.8071	0.2332	134	0.2032	2582	100
1.8071-1.856	0.2313	153	0.1898	2574	100
1.856-1.9106	0.2215	143	0.1861	2583	100
1.9106-1.9722	0.1857	151	0.1668	2560	100
1.9722-2.0427	0.2103	138	0.1698	2606	100
2.0427-2.1245	0.1845	137	0.167	2582	100
2.1245-2.2212	0.1859	142	0.1735	2581	100
2.2212-2.3383	0.2069	137	0.1703	2613	100
2.3383-2.4848	0.1889	149	0.1622	2613	100
2.4848-2.6766	0.1851	139	0.1765	2605	100
2.6766-2.946	0.2009	136	0.1754	2608	100
2.946-3.3721	0.1727	124	0.1699	2634	100
3.3721-4.2481	0.1559	129	0.1443	2641	100
4.2481-50	0.1616	127	0.1505	2720	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	2.7797	0.2337	1.4923	2.9005	1.6781	1.6374	0.0252	0.2251	-1.1871	0.152	0.1171	1.0956	1.3519	-0.8157	-0.1955	0.7663	-0.3591	0.0377	0.5766	-0.102	0.6695	9.6409	8.2788	-32.3753
2	2.0577	-0.3182	-0.7784	2.162	-0.1631	2.0472	-0.1471	0.1496	-0.3628	-0.1004	0.0268	0.1307	0.6359	-0.251	0.0885	0.3169	-0.0691	0.0105	0.1966	-0.016	0.2511	20.006	13.8564	-30.3361
3	3.8654	-0.2484	1.0129	1.8855	-0.2968	3.0583	-0.0272	0.4284	-0.3257	-0.4374	-0.0377	0.2275	0.3747	-0.5502	0.082	0.272	-0.096	-0.02	0.2736	-0.0268	0.1896	17.8819	18.7644	-39.3977
4	1.1565	-0.3144	-0.7099	1.6851	0.2284	4.427	-0.0729	0.2283	0.0929	-0.1001	0.0161	0.0285	0.1522	-0.0452	0.056	0.1303	-0.0437	-0.0079	0.1834	0.0146	0.1655	22.7231	24.2393	-34.1615
5	2.215	0.3259	-0.3638	1.5878	0.3659	3.0473	0.0267	0.1801	0.1086	-0.0525	0.0246	-0.0259	-0.0926	0.0072	-0.0553	0.1429	-0.0219	-0.0033	0.1914	0.0245	0.1707	26.2797	31.607	-32.6599
6	2.2044	-0.2187	0.5534	2.3558	0.4145	3.7447	-0.0738	0.2844	0.5455	-0.1154	0.0405	0.0781	-0.5175	-0.0618	0.0277	0.215	-0.004	0.0061	0.2058	0.079	0.3199	20.9526	43.1915	-32.7633
7	3.2743	0.7196	0.4757	2.8265	-0.4229	3.7941	0.0919	0.1068	0.7327	0.1609	-0.4436	0.0998	-1.3767	0.0965	0.3381	0.5903	-0.0257	-0.0995	0.2486	-0.0134	0.5439	25.3311	51.1241	-22.5051
8	0.7374	0.0056	-0.2833	2.4274	-4.0618	6.9094	0.3211	-0.1006	0.9303	0.1231	0.2495	0.6063	-1.3767	-0.3455	-0.5521	0.9935	0.1668	-0.1099	0.5237	-0.1063	0.9313	20.6513	53.8481	-23.2419
9	7.2134	1.1775	-2.1374	0.9243	-1.0692	2.1941	0.0902	0.2925	0.437	0.0116	-0.0219	-0.1181	-0.1161	0.1944	-0.0194	0.1672	-0.0161	-0.0187	0.5433	0.0523	0.3762	-0.0364	33.6842	-34.1034
10	2.3361	0.0901	1.094	0.1115	-0.1463	0.8727	0.1454	0.1584	0.187	-0.0025	-0.1696	0.2845	0.0106	-0.2557	0.0147	0.1746	-0.0049	-0.006	0.4299	0.0164	0.2927	4.0047	31.1408	-25.7276
11	3.2898	0.2651	0.9159	2.5393	1.1077	1.399	0.2881	-0.5664	-0.0885	0.3344	-0.2386	0.4143	0.1697	-0.712	-0.0487	0.2462	-0.0676	0.0221	0.4516	0.0323	0.2659	6.3466	29.8817	-18.8305
12	3.9928	0.7721	2.1755	2.1041	-0.5002	2.9409	0.0869	-0.4891	0.1472	0.2776	-0.0783	0.2258	-0.0061	-0.3455	-0.0195	0.1974	-0.027	0.0268	0.3258	-0.0071	0.201	17.2925	30.6947	-13.7676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 21 )	A	3 - 21
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 56 )	A	22 - 56
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 57 through 69 )	A	57 - 69
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 92 )	A	70 - 92
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 93 through 129 )	A	93 - 129
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 130 through 186 )	A	130 - 186
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 187 through 196 )	A	187 - 196
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 197 through 208 )	A	197 - 208
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 249 through 262 )	B	249 - 262
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 263 through 282 )	B	263 - 282
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 283 through 296 )	B	283 - 296
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 297 through 318 )	B	297 - 318

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