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- PDB-2lgx: NMR structure for Kindle-2 N-terminus -

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Basic information

Entry
Database: PDB / ID: 2lgx
TitleNMR structure for Kindle-2 N-terminus
ComponentsFermitin family homolog 2
KeywordsCELL ADHESION / Kindlin / membrane / integrin activation
Function / homology
Function and homology information


adherens junction maintenance / positive regulation of myosin light chain kinase activity / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / Cell-extracellular matrix interactions / type I transforming growth factor beta receptor binding / integrin activation / protein localization to membrane ...adherens junction maintenance / positive regulation of myosin light chain kinase activity / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / Cell-extracellular matrix interactions / type I transforming growth factor beta receptor binding / integrin activation / protein localization to membrane / focal adhesion assembly / negative regulation of vascular permeability / regulation of cell morphogenesis / I band / limb development / negative regulation of fat cell differentiation / SMAD binding / positive regulation of focal adhesion assembly / phosphatidylinositol-3,4,5-trisphosphate binding / lamellipodium membrane / RAC3 GTPase cycle / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / stress fiber / positive regulation of substrate adhesion-dependent cell spreading / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of stress fiber assembly / RAC1 GTPase cycle / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / positive regulation of GTPase activity / integrin-mediated signaling pathway / adherens junction / cytoplasmic side of plasma membrane / Wnt signaling pathway / positive regulation of protein localization to nucleus / actin filament binding / integrin binding / cell junction / actin binding / cell cortex / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cell adhesion / positive regulation of cell migration / focal adhesion / protein kinase binding / cell surface / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Fermitin family homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsPerera, H.D. / Ma, Y. / Yang, J. / Hirbawi, J. / Plow, E.F. / Qin, J.
CitationJournal: Structure / Year: 2011
Title: Membrane Binding of the N-Terminal Ubiquitin-Like Domain of kindlin-2 Is Crucial for Its Regulation of Integrin Activation.
Authors: Perera, H.D. / Ma, Y.Q. / Yang, J. / Hirbawi, J. / Plow, E.F. / Qin, J.
History
DepositionAug 3, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fermitin family homolog 2


Theoretical massNumber of molelcules
Total (without water)12,9881
Polymers12,9881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fermitin family homolog 2 / Kindlin-2 / Mitogen-inducible gene 2 protein / MIG-2 / Pleckstrin homology domain-containing family ...Kindlin-2 / Mitogen-inducible gene 2 protein / MIG-2 / Pleckstrin homology domain-containing family C member 1 / PH domain-containing family C member 1


Mass: 12987.990 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT2, KIND2, MIG2, PLEKHC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96AC1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HNCA
1713D H(CCO)NH
1813D C(CCO)NH
1913D (H)CCH-TOCSY
11013D 13C-15N NOESY
11122D 1H-1H TOCSY
11222D 1H-1H NOESY
11332D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM protein, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.1 mM [U-100% 15N] protein, 50 mM sodium phosphate, 100 mM sodium chloride, 0.05 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-100% 13C; U-100% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
0.05 %sodium azide-41
1 mMentity-52
50 mMsodium phosphate-62
100 mMsodium chloride-72
0.05 %sodium azide-82
0.1 mMentity-9[U-100% 15N]3
50 mMsodium phosphate-103
100 mMsodium chloride-113
0.05 %sodium azide-123
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
NMRViewJohnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
PASAXu, Wang, Yang, Vaynberg, Xu, and Qinchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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