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- PDB-1wlx: Solution structure of the third spectrin repeat of alpha-actinin-4 -

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Basic information

Entry
Database: PDB / ID: 1wlx
TitleSolution structure of the third spectrin repeat of alpha-actinin-4
ComponentsAlpha-actinin 4
KeywordsPROTEIN BINDING / three-helix bundle
Function / homology
Function and homology information


positive regulation of sodium:proton antiporter activity / negative regulation of substrate adhesion-dependent cell spreading / nucleoside binding / muscle cell development / nuclear retinoic acid receptor binding / vesicle transport along actin filament / Nephrin family interactions / cortical actin cytoskeleton / pseudopodium / retinoic acid receptor signaling pathway ...positive regulation of sodium:proton antiporter activity / negative regulation of substrate adhesion-dependent cell spreading / nucleoside binding / muscle cell development / nuclear retinoic acid receptor binding / vesicle transport along actin filament / Nephrin family interactions / cortical actin cytoskeleton / pseudopodium / retinoic acid receptor signaling pathway / stress fiber / tumor necrosis factor-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / nuclear receptor coactivator activity / platelet alpha granule lumen / cell projection / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / Z disc / positive regulation of non-canonical NF-kappaB signal transduction / actin filament binding / actin cytoskeleton / integrin binding / protein transport / Platelet degranulation / cell junction / actin binding / actin cytoskeleton organization / regulation of apoptotic process / transmembrane transporter binding / transcription coactivator activity / positive regulation of cell migration / ribonucleoprotein complex / focal adhesion / calcium ion binding / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsKowalski, K. / Merkel, A.L. / Booker, G.W.
CitationJournal: To be Published
Title: Solution structure of the third spectrin repeat of alpha-actinin-4
Authors: Kowalski, K. / Merkel, A.L. / Booker, G.W.
History
DepositionJun 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-actinin 4


Theoretical massNumber of molelcules
Total (without water)14,8381
Polymers14,8381
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Alpha-actinin 4 / Non-muscle alpha-actinin 4 / F-actin cross linking protein


Mass: 14837.590 Da / Num. of mol.: 1 / Fragment: third spectrin repeat (1-129)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN4 / Plasmid: pGEX-4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O43707

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
1333D 15N-separated NOESY
143HNHA
NMR detailsText: Assignments were obtained using HNCACB, CBCA(CO)NH, HNCO, H(CCO)NH-TOCSY, C(CO)NH-TOCSY, 15N NOESY-HSQC, 13C HSQC, 1H TOCSY, 1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6mM actinin-4; 25mM phosphate buffer; 100mM NaCl; 90% H2O, 10% D2O; 0.01% NaN390% H2O/10% D2O
20.6mM actinin-4; 25mM phosphate buffer; 100mM NaCl; 90% H2O, 10% D2O; 0.01% NaN3100% D2O
30.6mM actinin-4 U-15N; 25mM phosphate buffer; 100mM NaCl; 90% H2O, 10% D2O; 0.01% NaN390% H2O/10% D2O
40.6mM actinin-4 U-15N, 13C; 25mM phosphate buffer; 100mM NaCl; 90% H2O, 10% D2O; 0.01% NaN390% H2O/10% D2O
50.6mM actinin-4 U-15N, 13C; 25mM phosphate buffer; 100mM NaCl; 90% H2O, 10% D2O; 0.01% NaN3100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.75 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglio et alprocessing
Sparky3.11Goddard and Knellerdata analysis
CNS1.1Brunger et alstructure solution
ARIA1.2Linge and Nilgesstructure solution
ARIA1.2Linge and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: Structures are based on a total of 2256 restraints; 2021 NOE-derived distance constraints, 235 dihedral angle restraints
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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