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- PDB-1wku: High resolution structure of the human alpha-actinin isoform 3 -

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Basic information

Entry
Database: PDB / ID: 1wku
TitleHigh resolution structure of the human alpha-actinin isoform 3
ComponentsAlpha-actinin 3
KeywordsCONTRACTILE PROTEIN / Calponin homology domain / Actin binding domain
Function / homology
Function and homology information


positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / regulation of the force of skeletal muscle contraction / skeletal muscle atrophy / positive regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / transition between fast and slow fiber / positive regulation of bone mineralization involved in bone maturation ...positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / regulation of the force of skeletal muscle contraction / skeletal muscle atrophy / positive regulation of skeletal muscle fiber development / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / transition between fast and slow fiber / positive regulation of bone mineralization involved in bone maturation / muscle cell development / negative regulation of oxidative phosphorylation / focal adhesion assembly / Striated Muscle Contraction / bone morphogenesis / negative regulation of glycolytic process / Nephrin family interactions / negative regulation of cold-induced thermogenesis / negative regulation of calcineurin-NFAT signaling cascade / structural constituent of muscle / regulation of aerobic respiration / cortical actin cytoskeleton / pseudopodium / brush border / cell projection / actin filament / Z disc / actin filament binding / integrin binding / cell junction / actin cytoskeleton organization / regulation of apoptotic process / transmembrane transporter binding / focal adhesion / calcium ion binding / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Calponin-like domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...Calponin-like domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / 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. / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFranzot, G. / Sjoblom, B. / Gautel, M. / Djinovic Carugo, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The crystal structure of the actin binding domain from alpha-actinin in its closed conformation: structural insight into phospholipid regulation of alpha-actinin
Authors: Franzot, G. / Sjoblom, B. / Gautel, M. / Djinovic Carugo, K.
History
DepositionJun 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-actinin 3
B: Alpha-actinin 3


Theoretical massNumber of molelcules
Total (without water)58,5512
Polymers58,5512
Non-polymers00
Water8,269459
1
A: Alpha-actinin 3


Theoretical massNumber of molelcules
Total (without water)29,2761
Polymers29,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-actinin 3


Theoretical massNumber of molelcules
Total (without water)29,2761
Polymers29,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.499, 45.960, 66.998
Angle α, β, γ (deg.)86.67, 87.80, 87.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alpha-actinin 3 / Alpha actinin skeletal muscle isoform 3 / F-actin cross linking protein


Mass: 29275.564 Da / Num. of mol.: 2 / Fragment: actin binding domain (ABD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q08043
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: peg 20000, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: GRAPHITE MIRRORS
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→33.42 Å / Num. all: 56760 / Num. obs: 56760 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.5 Å2
Reflection shellResolution: 1.6→1.7 Å / % possible all: 87.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOW RESOLUTION MODEL OF DIFFERENT SPACE GROUP

Resolution: 1.6→33.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 197138 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 4024 7.1 %RANDOM
Rwork0.182 ---
obs0.182 56760 94 %-
all-56760 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7633 Å2 / ksol: 0.371786 e/Å3
Displacement parametersBiso mean: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-3 Å20.73 Å21.39 Å2
2--0.69 Å23.71 Å2
3----3.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 0 459 4085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 626 7.1 %
Rwork0.205 8218 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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