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- PDB-2k00: Solution structure of the talin F3 in complex with layilin cytodomain -

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Basic information

Entry
Database: PDB / ID: 2k00
TitleSolution structure of the talin F3 in complex with layilin cytodomain
Components
  • Layilin
  • Talin-1
KeywordsSTRUCTURAL PROTEIN / Cell projection / Cytoplasm / Cytoskeleton / Glycoprotein / Membrane / Phosphoprotein / Alternative splicing / Lectin / Transmembrane
Function / homology
Function and homology information


hyaluronic acid binding / ruffle / structural constituent of cytoskeleton / cell-cell adhesion / ruffle membrane / actin filament binding / integrin binding / carbohydrate binding / membrane => GO:0016020 / cytoskeleton ...hyaluronic acid binding / ruffle / structural constituent of cytoskeleton / cell-cell adhesion / ruffle membrane / actin filament binding / integrin binding / carbohydrate binding / membrane => GO:0016020 / cytoskeleton / focal adhesion / cell surface / plasma membrane / cytosol
Similarity search - Function
: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM ...: / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / Alpha-catenin/vinculin-like superfamily / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C-type lectin-like/link domain superfamily / FERM central domain / PH-domain like / C-type lectin fold / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsWegener, K.L. / Barsukov, I.L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis for the interaction between the cytoplasmic domain of the hyaluronate receptor layilin and the talin F3 subdomain
Authors: Wegener, K.L. / Basran, J. / Bagshaw, C.R. / Campbell, I.D. / Roberts, G.C. / Critchley, D.R. / Barsukov, I.L.
History
DepositionJan 23, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: Layilin


Theoretical massNumber of molelcules
Total (without water)12,3522
Polymers12,3522
Non-polymers00
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Talin-1


Mass: 10533.178 Da / Num. of mol.: 1 / Fragment: residues 309-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TLN1, TLN / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P54939
#2: Protein/peptide Layilin


Mass: 1818.938 Da / Num. of mol.: 1 / Fragment: residues 367-381 / Source method: obtained synthetically
Details: The peptide is the C-terminal layilin fragment naturally found in Mus musculus.
References: UniProt: Q8C351

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C filtered NOESY
1213D 1H-15N filtered NOESY
1312D 1H-1H filtered NOESY
NMR detailsText: The structure was determined using isotope-filtered experiments

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] protein, 3.5 mM peptide, 100 mM sodium chloride, 50 mM sodium phosphate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1[U-13C; U-15N]1
3.5 mMentity_21
100 mMsodium chloride1
50 mMsodium phosphate1
Sample conditionsIonic strength: 150 / pH: 6.1 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger A. T. et.al.refinement
ARIA1.2Linge, O'Donoghue and Nilgesstructure solution
TopSpin2Bruker Biospinprocessing
Analysis1CCPNdata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: Structure of the complex calculated using 127 intermolecular NOE and 155 NOEs within the peptide. Final structures refined in water.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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