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- PDB-2eyn: Crystal structure of the actin-binding domain of human alpha-acti... -

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Basic information

Entry
Database: PDB / ID: 2eyn
TitleCrystal structure of the actin-binding domain of human alpha-actinin 1 at 1.8 Angstrom resolution
ComponentsAlpha-actinin 1
KeywordsSTRUCTURAL PROTEIN / calponin homology domain / CH domain / Actin-binding / Actin-crosslinking / Actin-bundling
Function / homology
Function and homology information


platelet morphogenesis / structural constituent of postsynapse / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / actin filament network formation / vinculin binding / fascia adherens / muscle cell development / RHOF GTPase cycle / focal adhesion assembly / RHOD GTPase cycle ...platelet morphogenesis / structural constituent of postsynapse / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / actin filament network formation / vinculin binding / fascia adherens / muscle cell development / RHOF GTPase cycle / focal adhesion assembly / RHOD GTPase cycle / Nephrin family interactions / platelet formation / Syndecan interactions / cortical actin cytoskeleton / pseudopodium / brush border / actin filament bundle assembly / RHOBTB2 GTPase cycle / stress fiber / ruffle / nuclear receptor coactivator activity / platelet alpha granule lumen / cell projection / actin filament organization / Z disc / double-stranded RNA binding / cell-cell junction / actin filament binding / integrin binding / Platelet degranulation / cell junction / actin cytoskeleton organization / regulation of apoptotic process / transmembrane transporter binding / focal adhesion / glutamatergic synapse / calcium ion binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm / 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 / EF-hand domain / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. ...Calponin-like domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / EF-hand domain / 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 1, calcium-binding site / EF-hand calcium-binding domain. / 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: 1.8 Å
AuthorsBorrego-Diaz, E. / Kerff, F. / Lee, S.H. / Ferron, F. / Li, Y. / Dominguez, R.
CitationJournal: J.Struct.Biol. / Year: 2006
Title: Crystal structure of the actin-binding domain of alpha-actinin 1: Evaluating two competing actin-binding models.
Authors: Borrego-Diaz, E. / Kerff, F. / Lee, S.H. / Ferron, F. / Li, Y. / Dominguez, R.
History
DepositionNov 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-actinin 1


Theoretical massNumber of molelcules
Total (without water)26,5731
Polymers26,5731
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.007, 111.066, 31.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-373-

HOH

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Components

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


Mass: 26572.682 Da / Num. of mol.: 1 / Fragment: CH domain (residues 30-253)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN1 / Plasmid: pTYB12 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12814
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.746973 Å3/Da / Density % sol: 29.592518 %
Crystal growTemperature: 277.5 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 50mM NaCl, 1mM EDTA, 100mM imidazol, 24% PEG 5000 MME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 18533 / Num. obs: 17130 / % possible obs: 92.4 % / Redundancy: 5.8 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.901 / Net I/σ(I): 32.7
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1118 / Χ2: 0.921 / % possible all: 61.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human alpha-actinin 1 ABD, PDB 2EYI

2eyi


Resolution: 1.8→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 967 5.4 %random
Rwork0.184 ---
all0.194 ---
obs-16457 91.4 %-
Solvent computationBsol: 44.594 Å2
Displacement parametersBiso mean: 19.848 Å2
Baniso -1Baniso -2Baniso -3
1-2.663 Å20 Å20 Å2
2---2.127 Å20 Å2
3----0.536 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 156 1968
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.28
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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