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

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Basic information

Entry
Database: PDB / ID: 7d2s
TitleCrystal structure of Rsu1/PINCH1_LIM5C complex
Components
  • LIM and senescent cell antigen-like-containing domain protein 1
  • Ras suppressor protein 1
KeywordsPROTEIN 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 ...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 / cell-cell adhesion / positive regulation of GTPase activity / cell-cell junction / positive regulation of canonical NF-kappaB signal transduction / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / signal transduction / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Leucine-rich repeats, bacterial type ...: / : / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
LIM and senescent cell antigen-like-containing domain protein 1 / Ras suppressor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsYang, H. / Wei, Z. / Cong, Y.
Funding support China, 3items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionSep 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras suppressor protein 1
B: LIM and senescent cell antigen-like-containing domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1636
Polymers33,8482
Non-polymers3154
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-6 kcal/mol
Surface area13030 Å2
MethodPISA
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 number79
Space group name H-MI4

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Components

#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 / Glycerol


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 / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bicine pH8.5, 20% w/v PEG10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 46579 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 23.82 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.025 / Rrim(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 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.65-1.6812.90.93123210.8230.2690.9690.763
1.68-1.7113.60.79522910.8640.2230.8260.773
1.71-1.7413.60.69323490.90.1940.720.784
1.74-1.7813.50.58922910.9240.1660.6120.805
1.78-1.8213.40.48623150.9470.1370.5050.83
1.82-1.8613.10.38523130.9610.110.40.879
1.86-1.912.60.32823110.9670.0960.3420.938
1.9-1.9613.30.26523140.9810.0750.2761
1.96-2.0113.90.21923350.9870.0610.2271.106
2.01-2.0813.80.18823360.990.0530.1951.202
2.08-2.1513.50.16322830.9930.0460.1691.227
2.15-2.24130.14423310.9940.0420.151.28
2.24-2.3412.70.12423150.9940.0360.1291.377
2.34-2.4613.90.10923400.9960.030.1131.429
2.46-2.6213.80.123230.9960.0280.1031.331
2.62-2.8213.60.0923280.9950.0250.0931.214
2.82-3.1112.90.08223400.9970.0240.0851.079
3.11-3.5514.10.07323480.9980.020.0761.056
3.55-4.48130.06423790.9980.0180.0660.978
4.48-5013.30.06324160.9970.0180.0660.968

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1845 2355 5.06 %
Rwork0.166 44215 -
obs0.1669 46570 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.11 Å2 / Biso mean: 32.8943 Å2 / Biso min: 15.7 Å2
Refinement stepCycle: final / Resolution: 1.653→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 14 187 2376
Biso mean--32.17 38.82 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062293
X-RAY DIFFRACTIONf_angle_d1.0123115
X-RAY DIFFRACTIONf_chiral_restr0.042367
X-RAY DIFFRACTIONf_plane_restr0.005401
X-RAY DIFFRACTIONf_dihedral_angle_d12.833899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.653-1.68630.27141340.2411256197
1.6863-1.72290.24431430.21732546100
1.7229-1.7630.21711390.21532606100
1.763-1.80710.23321340.20322582100
1.8071-1.8560.23131530.18982574100
1.856-1.91060.22151430.18612583100
1.9106-1.97220.18571510.16682560100
1.9722-2.04270.21031380.16982606100
2.0427-2.12450.18451370.1672582100
2.1245-2.22120.18591420.17352581100
2.2212-2.33830.20691370.17032613100
2.3383-2.48480.18891490.16222613100
2.4848-2.67660.18511390.17652605100
2.6766-2.9460.20091360.17542608100
2.946-3.37210.17271240.16992634100
3.3721-4.24810.15591290.14432641100
4.2481-500.16161270.15052720100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.77970.23371.49232.90051.67811.63740.02520.2251-1.18710.1520.11711.09561.3519-0.8157-0.19550.7663-0.35910.03770.5766-0.1020.66959.64098.2788-32.3753
22.0577-0.3182-0.77842.162-0.16312.0472-0.14710.1496-0.3628-0.10040.02680.13070.6359-0.2510.08850.3169-0.06910.01050.1966-0.0160.251120.00613.8564-30.3361
33.8654-0.24841.01291.8855-0.29683.0583-0.02720.4284-0.3257-0.4374-0.03770.22750.3747-0.55020.0820.272-0.096-0.020.2736-0.02680.189617.881918.7644-39.3977
41.1565-0.3144-0.70991.68510.22844.427-0.07290.22830.0929-0.10010.01610.02850.1522-0.04520.0560.1303-0.0437-0.00790.18340.01460.165522.723124.2393-34.1615
52.2150.3259-0.36381.58780.36593.04730.02670.18010.1086-0.05250.0246-0.0259-0.09260.0072-0.05530.1429-0.0219-0.00330.19140.02450.170726.279731.607-32.6599
62.2044-0.21870.55342.35580.41453.7447-0.07380.28440.5455-0.11540.04050.0781-0.5175-0.06180.02770.215-0.0040.00610.20580.0790.319920.952643.1915-32.7633
73.27430.71960.47572.8265-0.42293.79410.09190.10680.73270.1609-0.44360.0998-1.37670.09650.33810.5903-0.0257-0.09950.2486-0.01340.543925.331151.1241-22.5051
80.73740.0056-0.28332.4274-4.06186.90940.3211-0.10060.93030.12310.24950.6063-1.3767-0.3455-0.55210.99350.1668-0.10990.5237-0.10630.931320.651353.8481-23.2419
97.21341.1775-2.13740.9243-1.06922.19410.09020.29250.4370.0116-0.0219-0.1181-0.11610.1944-0.01940.1672-0.0161-0.01870.54330.05230.3762-0.036433.6842-34.1034
102.33610.09011.0940.1115-0.14630.87270.14540.15840.187-0.0025-0.16960.28450.0106-0.25570.01470.1746-0.0049-0.0060.42990.01640.29274.004731.1408-25.7276
113.28980.26510.91592.53931.10771.3990.2881-0.5664-0.08850.3344-0.23860.41430.1697-0.712-0.04870.2462-0.06760.02210.45160.03230.26596.346629.8817-18.8305
123.99280.77212.17552.1041-0.50022.94090.0869-0.48910.14720.2776-0.07830.2258-0.0061-0.3455-0.01950.1974-0.0270.02680.3258-0.00710.20117.292530.6947-13.7676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 21 )A3 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 56 )A22 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 69 )A57 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 92 )A70 - 92
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 129 )A93 - 129
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 186 )A130 - 186
7X-RAY DIFFRACTION7chain 'A' and (resid 187 through 196 )A187 - 196
8X-RAY DIFFRACTION8chain 'A' and (resid 197 through 208 )A197 - 208
9X-RAY DIFFRACTION9chain 'B' and (resid 249 through 262 )B249 - 262
10X-RAY DIFFRACTION10chain 'B' and (resid 263 through 282 )B263 - 282
11X-RAY DIFFRACTION11chain 'B' and (resid 283 through 296 )B283 - 296
12X-RAY DIFFRACTION12chain 'B' and (resid 297 through 318 )B297 - 318

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