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- PDB-2r0o: Crystal structure of the actin-binding domain of human alpha-acti... -

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Basic information

Entry
Database: PDB / ID: 2r0o
TitleCrystal structure of the actin-binding domain of human alpha-actinin-4 mutant(K255E)
ComponentsAlpha-actinin-4
KeywordsActin-binding protein / CALPONIN HOMOLOGY DOMAIN / CH DOMAIN / STRUCTURAL 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 / vesicle transport along actin filament / nuclear retinoic acid receptor binding / 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 / vesicle transport along actin filament / nuclear retinoic acid receptor binding / 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 / protein transport / actin cytoskeleton / 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 / RNA binding / extracellular space / 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 / 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 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: 2.2 Å
AuthorsLee, S.H. / Dominguez, R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the actin-binding domain of alpha-actinin-4 Lys255Glu mutant implicated in focal segmental glomerulosclerosis.
Authors: Lee, S.H. / Weins, A. / Hayes, D.B. / Pollak, M.R. / Dominguez, R.
History
DepositionAug 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-actinin-4
B: Alpha-actinin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6256
Polymers54,2562
Non-polymers3684
Water8,233457
1
A: Alpha-actinin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2202
Polymers27,1281
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-actinin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4044
Polymers27,1281
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.697, 61.533, 174.936
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 / F-actin cross-linking protein


Mass: 27128.062 Da / Num. of mol.: 2 / Fragment: ALPHA-ACTININ-4 (residues 47-271) / Mutation: K255E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: HUMAN / Gene: ACTN4 / Plasmid: pGEX-4T1-HTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43707
#2: Chemical
ChemComp-GOL / GLYCEROL / Non-muscle alpha-actinin 4 / F-actin cross-linking protein / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 100 mM Imidazole, 50 mM NaCl, 1 mM EDTA, 5 % (v/v) glycerol, and 21 % (w/v) polyethylene glycol 5000 mono-methyl-ether, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2007 / Details: MIRROR
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→42.4 Å / Num. all: 25757 / Num. obs: 25757 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 33.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 6.6 / Num. unique all: 1298 / Rsym value: 0.283 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EYI

2eyi


Resolution: 2.2→42.37 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.654 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: FOUR TLS GROUPS (TWO CH1 AND TWO CH2 DOMAINS)
Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22388 1513 5.1 %RANDOM
Rwork0.17142 ---
all0.17427 25757 --
obs0.17427 22537 87.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.413 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 24 457 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223882
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9565252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4975482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83424.197193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23415729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2851530
X-RAY DIFFRACTIONr_chiral_restr0.1080.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022914
X-RAY DIFFRACTIONr_nbd_refined0.1980.21753
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2319
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.218
X-RAY DIFFRACTIONr_mcbond_it0.7581.52405
X-RAY DIFFRACTIONr_mcangle_it1.17423748
X-RAY DIFFRACTIONr_scbond_it1.90631707
X-RAY DIFFRACTIONr_scangle_it2.9544.51490
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 77 -
Rwork0.183 1536 -
obs-1536 69.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08890.77010.0023.0947-0.5921.0196-0.10450.1023-0.135-0.19760.0828-0.11010.06990.01630.0217-0.0472-0.0152-0.0001-0.0612-0.0207-0.067.7635-10.252239.6238
22.58121.7008-1.29743.4875-1.04942.67970.11230.01380.0046-0.19930.0165-0.203-0.14430.2856-0.1287-0.0719-0.04550.0377-0.0653-0.0154-0.064622.90359.610533.3332
31.8268-0.41670.60860.8875-0.40642.3408-0.0258-0.2105-0.0364-0.0374-0.0654-0.1118-0.04780.09420.0913-0.1180.0176-0.00770.0650.0588-0.10530.6197-11.073479.2792
42.263-0.15930.3791.7204-0.83773.4963-0.0873-0.2630.0654-0.01080.07940.0661-0.2737-0.48890.008-0.09260.0884-0.01760.0266-0.0144-0.10879.9417-2.006566.8879
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA46 - 1577 - 118
2X-RAY DIFFRACTION2AA158 - 272119 - 233
3X-RAY DIFFRACTION3BB44 - 1575 - 118
4X-RAY DIFFRACTION4BB158 - 272119 - 233

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