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- PDB-7lt9: Crystal structure of Ras suppressor-1 in complex with PINCH-1 LIM... -

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Basic information

Entry
Database: PDB / ID: 7lt9
TitleCrystal structure of Ras suppressor-1 in complex with PINCH-1 LIM4-5 domains
Components
  • LIM and senescent cell antigen-like-containing domain protein 1
  • Ras suppressor protein 1
KeywordsCELL ADHESION / leucine-rich repeat LIM domain
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 GTPase activity / positive regulation of focal adhesion assembly / cellular response to transforming growth factor beta stimulus / positive regulation of substrate adhesion-dependent cell spreading / tumor necrosis factor-mediated signaling pathway ...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 GTPase activity / positive regulation of focal adhesion assembly / cellular response to transforming growth factor beta stimulus / positive regulation of substrate adhesion-dependent cell spreading / tumor necrosis factor-mediated signaling pathway / establishment of protein localization / cell-cell adhesion / cell-cell junction / actin binding / positive regulation of canonical NF-kappaB signal transduction / intracellular 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 / cytoplasm / cytosol
Similarity search - Function
LIM and senescent cell antigen-like-containing domain protein 1-like / : / : / : / 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. / : ...LIM and senescent cell antigen-like-containing domain protein 1-like / : / : / : / 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 repeat region / 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 / molecular replacement / Resolution: 3.05011197028 Å
AuthorsFukuda, K. / Qin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular basis for Ras suppressor-1 binding to PINCH-1 in focal adhesion assembly.
Authors: Fukuda, K. / Lu, F. / Qin, J.
History
DepositionFeb 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 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)48,3126
Polymers48,0512
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-6 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.042, 144.384, 185.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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Components

#1: Protein Ras suppressor protein 1 / RSP-1 / Rsu-1


Mass: 31861.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RSU1, RSP1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf-9 / 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: 16189.122 Da / Num. of mol.: 1 / Fragment: LIM domain (UNP residues 193-329)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1, PINCH, PINCH1 / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P48059
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.66 Å3/Da / Density % sol: 66.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 7.5 / Details: PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 29, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.05011197028→50 Å / Num. obs: 13446 / % possible obs: 97.1 % / Redundancy: 4.6 % / Biso Wilson estimate: 67.4053598249 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.091 / Net I/σ(I): 27.76225
Reflection shellResolution: 3.05011197028→3.1 Å / Rmerge(I) obs: 0.852 / Num. unique obs: 669 / CC1/2: 0.731 / CC star: 0.919 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7LT8

7lt8


Resolution: 3.05011197028→34.5707614021 Å / SU ML: 0.399321051542 / Cross valid method: THROUGHOUT / σ(F): 1.33638551595 / Phase error: 23.6012965098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.234347851614 649 4.95911973714 %RANDOM
Rwork0.199707401939 12438 --
obs0.201444108787 13087 96.6829196217 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.314907178 Å2
Refinement stepCycle: LAST / Resolution: 3.05011197028→34.5707614021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 4 0 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01492221090233146
X-RAY DIFFRACTIONf_angle_d1.165670582164229
X-RAY DIFFRACTIONf_chiral_restr0.0595704202459474
X-RAY DIFFRACTIONf_plane_restr0.00645066029694544
X-RAY DIFFRACTIONf_dihedral_angle_d16.37946568581911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05011197028-3.28540.3367955478241410.2752451711122478X-RAY DIFFRACTION99.3927893738
3.2854-3.61580.3384296686211460.2355954882512X-RAY DIFFRACTION99.1421111526
3.6158-4.13820.2276504718661180.2050550092732477X-RAY DIFFRACTION97.1546237364
4.1382-5.21080.1892154804061280.1783677414692478X-RAY DIFFRACTION95.985267035

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