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- PDB-2k9u: Solution NMR structure of the Filamin-migfilin complex -

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Basic information

Entry
Database: PDB / ID: 2k9u
TitleSolution NMR structure of the Filamin-migfilin complex
Components
  • Filamin-binding LIM protein 1
  • Gamma filamin
KeywordsSTRUCTURAL PROTEIN / cytoskeletal complex / Cell adhesion / Cell junction / Cell shape / Cytoskeleton / LIM domain / Metal-binding
Function / homology
Function and homology information


regulation of integrin activation / filamin binding / Cell-extracellular matrix interactions / costamere / sarcomere organization / ankyrin binding / intercellular bridge / stress fiber / cytoskeletal protein binding / cell periphery ...regulation of integrin activation / filamin binding / Cell-extracellular matrix interactions / costamere / sarcomere organization / ankyrin binding / intercellular bridge / stress fiber / cytoskeletal protein binding / cell periphery / sarcolemma / cell-cell adhesion / fibrillar center / Z disc / actin filament binding / cell junction / regulation of cell shape / cytoskeleton / focal adhesion / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...Filamin family / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-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. / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Filamin-C / Gamma filamin variant / Filamin-binding LIM protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsIthychanda, S.N. / Qin, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Migfilin, a molecular switch in regulation of integrin activation.
Authors: Ithychanda, S.S. / Das, M. / Ma, Y.Q. / Ding, K. / Wang, X. / Gupta, S. / Wu, C. / Plow, E.F. / Qin, J.
History
DepositionOct 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 3, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma filamin
B: Filamin-binding LIM protein 1


Theoretical massNumber of molelcules
Total (without water)15,0962
Polymers15,0962
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 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Gamma filamin / Filamin-C / Filamin-2 / Protein FLNc / Actin-binding-like protein / ABP-L / ABP-280-like protein


Mass: 12434.720 Da / Num. of mol.: 1 / Fragment: UNP residues 919-1032
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX5x-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59H94, UniProt: Q14315*PLUS
#2: Protein/peptide Filamin-binding LIM protein 1 / FBLP-1 / Mitogen-inducible 2-interacting protein / MIG2-interacting protein / Migfilin


Mass: 2661.150 Da / Num. of mol.: 1 / Fragment: UNP residues 1-24 / Source method: obtained synthetically
Details: Synthetic peptide of the sequence corresponding to residues 1-24 of human Filamin-binding LIM protein 1, UniProt entry Q8WUP2, FBLI1_HUMAN
References: UniProt: Q8WUP2
Sequence detailsTHE N-TERMINAL RESIDUES GIPEF ARE THE EXPRESSION TAG FROM THE PLASMID VECTOR USED TO EXPRESS THE PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D HN(CA)CB

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Sample preparation

DetailsContents: 0.1-1 mM [U-100% 13C; U-100% 15N] entity_1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: entity_1 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 0.1-1
Sample conditionsIonic strength: 0.025 / pH: 6.4 / Pressure: ambient / Temperature: 302 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLORSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 1. The regions 1-15 and 109-119 of entity 1 (chain A), because they are not part of Ig (immunoglobulin-like) domain, have few contraints and are essentially unfolded. 2. In entity 2 (chain B ...Details: 1. The regions 1-15 and 109-119 of entity 1 (chain A), because they are not part of Ig (immunoglobulin-like) domain, have few contraints and are essentially unfolded. 2. In entity 2 (chain B peptide), the regions 1-6 and 18-24 do not have many constraints and seem unfolded.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 20

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