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- PDB-6oa6: CRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF HUMAN ALPHA-ACTININ-4 -

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Basic information

Entry
Database: PDB / ID: 6oa6
TitleCRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF HUMAN ALPHA-ACTININ-4
ComponentsAlpha-actinin-4
KeywordsSTRUCTURAL PROTEIN / CALPONIN HOMOLOGY DOMAIN / CH DOMAIN / ACTIN- BINDING PROTEIN / ACTIN-CROSSLINKING / GLOMERULOSCLEROS SPECTRIN FAMILY / DISEASE MUTATION / NUCLEUS / PHOSPHORYLATION
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 / protein transport / integrin binding / 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
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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site ...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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / 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: 1.37 Å
AuthorsBirrane, G. / Feng, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK59588 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK114329 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK007199 United States
CitationJournal: J. Am. Soc. Nephrol. / Year: 2020
Title: Phosphorylation of ACTN4 Leads to Podocyte Vulnerability and Proteinuric Glomerulosclerosis.
Authors: Feng, D. / Kumar, M. / Muntel, J. / Gurley, S.B. / Birrane, G. / Stillman, I.E. / Ding, L. / Wang, M. / Ahmed, S. / Schlondorff, J. / Alper, S.L. / Ferrante, T. / Marquez, S.L. / Ng, C.F. / ...Authors: Feng, D. / Kumar, M. / Muntel, J. / Gurley, S.B. / Birrane, G. / Stillman, I.E. / Ding, L. / Wang, M. / Ahmed, S. / Schlondorff, J. / Alper, S.L. / Ferrante, T. / Marquez, S.L. / Ng, C.F. / Novak, R. / Ingber, D.E. / Steen, H. / Pollak, M.R.
History
DepositionMar 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-actinin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8342
Polymers26,7421
Non-polymers921
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.589, 61.732, 89.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-actinin-4 / / Non-muscle alpha-actinin 4


Mass: 26741.730 Da / Num. of mol.: 1 / Mutation: S159D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN4 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43707
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50mM Sodium Chloride, 5% Glycerol, 1mM EDTA, 15 - 18% PEG5000-MME
PH range: 7.2 - 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0719 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2016 / Details: MIRROR
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0719 Å / Relative weight: 1
ReflectionResolution: 1.37→50.83 Å / Num. obs: 52645 / % possible obs: 97.7 % / Redundancy: 5.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.048 / Net I/σ(I): 17.8
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.44 / Num. unique obs: 2441 / CC1/2: 0.667 / Rpim(I) all: 0.048 / % possible all: 91.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R0O

2r0o


Resolution: 1.37→36.7 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.793 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 2579 4.9 %RANDOM
Rwork0.13416 ---
obs0.13615 49955 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.031 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å20 Å2-0 Å2
2---1.91 Å20 Å2
3----1.57 Å2
Refinement stepCycle: 1 / Resolution: 1.37→36.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 6 292 2134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122000
X-RAY DIFFRACTIONr_bond_other_d0.0030.0171916
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6352716
X-RAY DIFFRACTIONr_angle_other_deg0.5831.5674459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9365255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92422.589112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16715382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3591514
X-RAY DIFFRACTIONr_chiral_restr0.0870.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022253
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7231.911955
X-RAY DIFFRACTIONr_mcbond_other1.7191.907953
X-RAY DIFFRACTIONr_mcangle_it2.182.8791201
X-RAY DIFFRACTIONr_mcangle_other2.1792.8821202
X-RAY DIFFRACTIONr_scbond_it2.8832.3621045
X-RAY DIFFRACTIONr_scbond_other2.8822.3621046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2863.3811505
X-RAY DIFFRACTIONr_long_range_B_refined3.94824.6542402
X-RAY DIFFRACTIONr_long_range_B_other3.75723.6892334
X-RAY DIFFRACTIONr_rigid_bond_restr5.833916
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.371→1.406 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 148 -
Rwork0.294 3432 -
obs--91.65 %

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