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- PDB-1nyp: 4th LIM domain of PINCH protein -

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Basic information

Entry
Database: PDB / ID: 1nyp
Title4th LIM domain of PINCH protein
ComponentsPINCH protein
KeywordsCELL ADHESION / LIM domain / protein recognition
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 / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / Cysteine Rich Protein / Cysteine Rich Protein / 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. / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM and senescent cell antigen-like-containing domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVelyvis, A. / Vaynberg, J. / Vinogradova, O. / Zhang, Y. / Wu, C. / Qin, J.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structural and functional insights into PINCH LIM4 domain-mediated integrin signaling
Authors: Velyvis, A. / Vaynberg, J. / Yang, Y. / Vinogradova, O. / Zhang, Y. / Wu, C. / Qin, J.
History
DepositionFeb 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PINCH protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6643
Polymers7,5331
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein PINCH protein / LIM and senescent cell antigen-like domains 1


Mass: 7532.742 Da / Num. of mol.: 1 / Fragment: 4th LIM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48059
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D-15N,13C-edited-NOESY

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Sample preparation

DetailsContents: 1.7 mM U-15N,13C-LIM4; 95% H2O, 5% D2O / Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 0.13 / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz

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Processing

NMR software
NameClassification
NMRPipeprocessing
PIPPdata analysis
X-PLORstructure solution
X-PLORrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: SA protocol without Zn cofactors starting from linear protein structure, followed by addition of Zn into structures and minimization
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 20

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