PDB-7d2t: Crystal structure of Rsu1/PINCH1_LIM45C complex

ID or keywords:

Entry

Database: PDB / ID: 7d2t

Title

Crystal structure of Rsu1/PINCH1_LIM45C 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 / positive regulation of substrate adhesion-dependent cell spreading / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / establishment of protein localization ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Yang, H. / Wei, Z. / Yu, C.

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	31870757	China
National Natural Science Foundation of China (NSFC)	31970741	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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7d2t.cif.gz	331.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7d2t.ent.gz	267.5 KB	Display	PDB format
PDBx/mmJSON format	7d2t.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/d2/7d2t ftp://data.pdbj.org/pub/pdb/validation_reports/d2/7d2t	HTTPS FTP

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Related structure data

Related structure data	7d2sSC 7d2uC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3lml-3 7d2u-d 5t1j-3 3lml-2 3lml-1 5t1j-2 3t79-2 2sli-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	#143 - Nov 2011 Toll-like Receptors similarity (5) #248 - Aug 2020 Phytosulfokine Receptor similarity (5) #245 - May 2020 Spliceosomes similarity (3) #68 - Aug 2005 Neurotrophins similarity (2) #105 - Sep 2008 Ribonuclease A similarity (2)

Deposited unit

A: Ras suppressor protein 1

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

C: Ras suppressor protein 1

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

hetero molecules

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

1

A: Ras suppressor protein 1

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

hetero molecules

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

2

C: Ras suppressor protein 1

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

hetero molecules

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

Unit cell

Length a, b, c (Å)	114.624, 51.293, 119.626
Angle α, β, γ (deg.)	90.000, 101.550, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 2 types, 4 molecules ACBD

#1: Protein	Ras suppressor protein 1 / Rsu-1 Mass: 31982.713 Da / Num. of mol.: 2 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: 16248.257 Da / Num. of mol.: 2 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

#1: Protein

Ras suppressor protein 1 / Rsu-1

Mass: 31982.713 Da / Num. of mol.: 2
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: 16248.257 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 375 molecules

#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 3.57 Å³/Da / Density % sol: 65.56 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium malonate pH7.0, 12% w/v Polyethylene glycol 3350

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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: Apr 7, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 70288 / % possible obs: 100 % / Redundancy: 6.7 % / B_iso Wilson estimate: 40.74 Å² / R_merge(I) obs: 0.152 / R_pim(I) all: 0.064 / R_rim(I) all: 0.165 / Χ²: 1.119 / Net I/σ(I): 4.8

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.24	6.9	1.204	3504	0.687	0.49	1.301	0.772	100
2.24-2.28	6.9	0.993	3436	0.744	0.407	1.074	0.803	100
2.28-2.32	6.8	0.834	3522	0.806	0.343	0.903	0.798	100
2.32-2.37	6.7	0.708	3476	0.828	0.294	0.768	0.813	100
2.37-2.42	6.6	0.617	3472	0.844	0.259	0.67	0.818	99.9
2.42-2.48	6.2	0.514	3483	0.894	0.224	0.562	0.862	99.9
2.48-2.54	6.4	0.457	3479	0.917	0.195	0.498	0.891	99.9
2.54-2.61	6.9	0.398	3528	0.933	0.162	0.43	0.929	99.9
2.61-2.69	7	0.343	3468	0.946	0.139	0.37	0.968	100
2.69-2.77	7	0.294	3490	0.956	0.119	0.318	1.038	100
2.77-2.87	6.9	0.25	3539	0.969	0.102	0.27	1.098	100
2.87-2.99	6.9	0.225	3457	0.968	0.092	0.243	1.133	100
2.99-3.12	6.7	0.194	3489	0.973	0.081	0.211	1.194	100
3.12-3.29	6.2	0.159	3532	0.981	0.07	0.174	1.247	100
3.29-3.49	6.9	0.146	3539	0.983	0.06	0.158	1.316	100
3.49-3.76	7	0.126	3512	0.987	0.051	0.136	1.425	100
3.76-4.14	6.8	0.116	3529	0.987	0.048	0.125	1.548	99.9
4.14-4.74	6.3	0.11	3556	0.983	0.048	0.12	1.552	99.9
4.74-5.97	6.7	0.111	3571	0.99	0.047	0.121	1.621	99.9
5.97-50	6.3	0.1	3706	0.992	0.043	0.109	1.562	99.9

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7D2S

7d2s

Resolution: 2.2→50 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1978	2008	2.86 %
R_work	0.1701	68220	-
obs	0.1709	70228	99.74 %

Solvent computation

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

Displacement parameters

B_iso max: 152.94 Å² / B_iso mean: 53.2771 Å² / B_iso min: 19.62 Å²

Refinement step

Cycle: final / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6038	0	74	358	6470
B_iso mean	-	-	78.1	52	-
Num. residues	-	-	-	-	753

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6244
X-RAY DIFFRACTION	f_angle_d	0.735	8434
X-RAY DIFFRACTION	f_chiral_restr	0.027	941
X-RAY DIFFRACTION	f_plane_restr	0.003	1081
X-RAY DIFFRACTION	f_dihedral_angle_d	12.464	2373

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 (%)
2.2-2.25	0.3076	152	0.2813	4728	98
2.25-2.3108	0.2675	134	0.2427	4818	100
2.3108-2.3788	0.2659	145	0.2291	4838	100
2.3788-2.4556	0.2511	143	0.2132	4870	100
2.4556-2.5433	0.2271	143	0.2103	4847	100
2.5433-2.6452	0.2734	139	0.2071	4824	100
2.6452-2.7655	0.2609	140	0.1955	4855	100
2.7655-2.9113	0.2244	147	0.1907	4877	100
2.9113-3.0937	0.2461	137	0.1975	4883	100
3.0937-3.3325	0.2216	141	0.1884	4868	100
3.3325-3.6678	0.1849	147	0.1689	4935	100
3.6678-4.1983	0.1627	141	0.1402	4878	100
4.1983-5.2883	0.1512	151	0.1298	4929	100
5.2883-48.15	0.1666	148	0.1469	5070	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	4.6142	-0.4868	0.5317	3.5444	1.7881	3.0382	0.1088	0.9448	-0.0099	-1.592	-0.3575	2.0973	-0.534	-1.8646	0.1209	0.8783	-0.0078	-0.2729	1.1799	0.0996	1.1226	26.2538	8.2723	-6.0634
2	3.0927	-1.0102	1.3341	2.7954	-0.9966	3.7078	0.0098	0.0228	0.135	-0.0381	0.0187	0.175	-0.1645	-0.1645	-0.0221	0.2885	0.0042	0.0123	0.1582	-0.0014	0.2384	49.1907	7.7772	4.5493
3	9.304	0.4615	0.3537	3.2804	-1.0981	5.4029	0.1012	-0.6702	-0.3141	0.4788	0.0492	0.0886	-0.045	-0.288	-0.1322	0.3772	0.0124	-0.0665	0.2961	0.0342	0.2032	59.8059	-3.7624	25.393
4	6.2791	4.8563	-0.9386	4.8215	-0.3819	2.2507	0.0961	0.4678	-0.2131	0.0686	0.1054	-0.2787	-0.1269	0.2063	-0.1717	0.3947	0.0387	-0.0641	0.5537	0.0292	0.3364	68.0666	-0.123	32.3572
5	6.094	-0.2608	-1.5249	9.9819	6.0144	5.3691	-0.8612	-0.3516	0.3658	0.4353	0.0483	0.4835	0.2448	0.9924	0.8741	0.8532	-0.157	0.1505	1.2721	-0.1945	0.7578	30.5905	21.6596	55.8009
6	9.8254	-6.6174	-5.0169	7.8546	4.6976	3.9813	0.9355	-0.5795	1.4772	0.5076	0.5012	-0.4657	-2.4131	0.2064	-1.3893	1.0627	-0.13	0.3476	0.8706	-0.2115	0.7613	32.2932	24.3905	43.1299
7	6.5898	3.149	1.0421	9.6127	-2.6893	6.0885	0.6845	-1.4173	0.832	0.1145	-0.529	0.4345	-0.5023	0.3142	-0.2454	0.6255	-0.0253	0.2441	0.7503	-0.0493	0.5705	29.0766	16.9617	40.8294
8	2.2064	-0.5081	-2.3866	4.2262	3.0725	2.7216	-0.006	-0.3984	0.0847	0.5083	-0.0604	0.6624	-0.0787	-0.3783	0.0829	0.4312	0.0757	0.1045	0.5605	0.0547	0.4784	33.3306	5.4431	20.9909
9	4.9826	-2.225	-3.4028	7.2782	1.9405	6.4677	-0.1054	-0.3211	-0.661	0.0497	0.093	0.6389	0.7115	-0.2705	0.0204	0.353	-0.0749	-0.0227	0.2631	0.0752	0.362	45.0335	-10.4896	8.7601
10	7.2933	-1.8185	-0.5057	8.2396	1.953	2.0201	-0.1329	2.6179	-0.9308	-3.2342	-0.0232	1.2758	-0.513	-1.4462	0.1555	1.3805	-0.253	-0.1931	1.4086	0.0175	0.8171	-12.3104	10.8699	27.2279
11	3.7754	1.013	1.7814	3.6442	1.1614	4.3848	0.0023	0.197	-0.1332	-0.1896	-0.0203	0.0178	0.1536	0.004	0.0151	0.2163	0.0124	0.0032	0.2142	-0.0051	0.2364	-6.2586	11.301	51.2961
12	7.3842	-1.2047	2.2679	5.0343	0.4394	8.6736	-0.0712	-0.1326	-0.2523	0.1776	0.1052	-0.4078	-0.0534	1.0003	-0.0521	0.2226	-0.0212	-0.0552	0.3647	-0.0213	0.33	14.4308	20.7086	69.0383
13	3.7806	-1.5311	-1.5514	3.2205	3.156	3.6009	0.4774	-0.7016	-0.2845	-0.1408	0.1333	0.1513	-0.0345	0.0966	-0.6278	0.7979	0.046	0.0618	1.1043	0.1124	0.7046	49.1928	-6.311	42.0379
14	6.0098	-8.3574	-1.7765	2.0055	1.9769	3.0128	-0.1045	-0.4988	0.5399	-0.0656	0.5131	-0.4207	0.0704	0.0635	-0.4073	0.5705	0.0939	0.1478	1.1441	0.1418	0.9143	43.272	-1.8602	39.9506
15	4.5009	-6.216	-1.9885	2.0197	4.8089	3.9748	-0.675	-0.8526	-1.1198	-0.5681	-0.3501	-0.3655	0.8624	0.4331	0.9031	0.6156	0.1437	0.2618	0.8289	0.1864	0.9097	32.4946	-3.0339	37.4405
16	5.9206	-4.6211	3.2774	7.5683	2.4791	8.6168	-0.0212	-0.7051	-0.6093	0.2843	-0.3421	0.5382	-0.2806	0.6782	0.2948	0.5228	-0.0071	0.1915	0.8501	0.0952	0.58	27.2479	3.9874	40.9671
17	2.0334	-1.2289	-0.5354	4.1732	-2.1017	1.2302	-0.125	0.5472	-0.3648	-1.148	0.3161	-0.5521	0.1084	1.0402	-0.1477	0.4946	0.0404	0.1491	0.806	-0.1187	0.4585	11.9084	10.2271	38.3263
18	7.3779	-2.1409	-2.6423	6.2378	-1.7	8.1785	0.105	0.7117	0.474	-0.8582	0.0489	-0.6663	-0.269	0.8345	-0.1392	0.4665	-0.0623	0.0933	0.5202	-0.0271	0.3635	6.48	20.6202	37.5335
19	8.1769	-5.5014	0.4701	2.0853	0.6978	8.9852	0.0751	0.6843	0.6321	-0.5845	-0.0735	-0.2697	-0.6801	0.4425	-0.0029	0.3749	-0.0942	-0.0218	0.3403	0.0487	0.327	0.4124	27.0465	44.4001
20	2.0406	-1.953	-0.565	2.0294	2.9171	2.0342	-0.3271	-0.1633	0.7614	-0.1747	-0.0539	-0.6903	-0.7628	0.8374	0.5038	0.3806	-0.0296	-0.0728	0.3016	0.0516	0.4058	-3.7485	32.7032	53.2753

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 5 through 21 )	A	5 - 21
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 186 )	A	22 - 186
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 187 through 228 )	A	187 - 228
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 229 through 251 )	A	229 - 251
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 189 through 213 )	B	189 - 213
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 214 through 223 )	B	214 - 223
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 224 through 236 )	B	224 - 236
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 237 through 290 )	B	237 - 290
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 291 through 317 )	B	291 - 317
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 5 through 21 )	C	5 - 21
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 22 through 186 )	C	22 - 186
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 187 through 251 )	C	187 - 251
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 189 through 203 )	D	189 - 203
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 204 through 216 )	D	204 - 216
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 217 through 231 )	D	217 - 231
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 232 through 248 )	D	232 - 248
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 249 through 262 )	D	249 - 262
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 263 through 290 )	D	263 - 290
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 291 through 306 )	D	291 - 306
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 307 through 317 )	D	307 - 317

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Protein , 2 types, 4 molecules ACBD

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Non-polymers , 5 types, 375 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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

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Yorodumi