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- PDB-5a4b: Mutations in the Calponin homology domain of Alpha-Actinin-2 affe... -

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Basic information

Entry
Database: PDB / ID: 5a4b
TitleMutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle.
ComponentsHUMAN ALPHA-ACTININ-2
KeywordsSTRUCTURAL PROTEIN / CALPONIN HOMOLOGY DOMAINS
Function / homology
Function and homology information


actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / positive regulation of cation channel activity / LIM domain binding ...actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / negative regulation of protein localization to cell surface / positive regulation of cation channel activity / LIM domain binding / microspike assembly / postsynaptic actin cytoskeleton / positive regulation of potassium ion transport / muscle cell development / focal adhesion assembly / Striated Muscle Contraction / Assembly and cell surface presentation of NMDA receptors / Nephrin family interactions / cardiac muscle cell development / structural constituent of muscle / sarcomere organization / cortical actin cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / negative regulation of potassium ion transport / Long-term potentiation / postsynaptic density, intracellular component / titin binding / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / nuclear receptor coactivator activity / platelet alpha granule lumen / filopodium / protein localization to plasma membrane / cell projection / actin filament / postsynaptic density membrane / Z disc / actin filament binding / integrin binding / cell junction / Platelet degranulation / actin cytoskeleton organization / RAF/MAP kinase cascade / regulation of apoptotic process / transmembrane transporter binding / dendritic spine / cytoskeleton / cell adhesion / protein domain specific binding / focal adhesion / glutamatergic synapse / calcium ion binding / extracellular exosome / extracellular region / identical protein binding / cytosol
Similarity search - Function
Calponin-like domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. ...Calponin-like domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / 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 domain pair / 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 / OTHER / Resolution: 2.01 Å
AuthorsHaywood, N.J. / Wolny, M. / Trinh, C.H. / Shuping, Y. / Edwards, T.A. / Peckham, M.
CitationJournal: Biochem.J. / Year: 2016
Title: Hypertrophic Cardiomyopathy Mutations in the Calponin-Homology Domain of Actn2 Affect Actin Binding and Cardiomyocyte Z-Disc Incorporation.
Authors: Haywood, N. / Wolny, M. / Rogers, B. / Trinh, C.H. / Shuping, Y. / Edwards, T.A. / Peckham, M.
History
DepositionJun 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN ALPHA-ACTININ-2
B: HUMAN ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)56,9262
Polymers56,9262
Non-polymers00
Water3,621201
1
A: HUMAN ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)28,4631
Polymers28,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HUMAN ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)28,4631
Polymers28,4631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.390, 46.630, 69.860
Angle α, β, γ (deg.)73.80, 80.02, 75.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HUMAN ALPHA-ACTININ-2 / ALPHA-ACTININ SKELETAL MUSCLE ISOFORM 2 / F-ACTIN CROSS-LINKING PROTEIN / HUMAN ALPHA-ACTININ-2


Mass: 28462.750 Da / Num. of mol.: 2 / Fragment: CALPONIN HOMOLOGY DOMAIN, RESIDUES 19-266 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35609
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDOMAIN CONTAINING RESIDUES 19 TO 266. POINT MUTATION A119T AT POSITION 119.

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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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 7.5 / Details: 24% POLYETHYLENE GLYCOL 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→66.68 Å / Num. obs: 28251 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.2
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.2 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.01→66.68 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.603 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23464 1404 5 %RANDOM
Rwork0.19756 ---
obs0.19943 26847 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å20.24 Å20.19 Å2
2--0.33 Å21.6 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.01→66.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 0 201 3789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193660
X-RAY DIFFRACTIONr_bond_other_d0.0020.023604
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9554940
X-RAY DIFFRACTIONr_angle_other_deg0.96438294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63324.286168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85115692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6821524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024066
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02826
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_it1.3792.1971782
X-RAY DIFFRACTIONr_mcbond_other1.3792.1961781
X-RAY DIFFRACTIONr_mcangle_it2.2293.2872224
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6912.4181878
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 105 -
Rwork0.262 1948 -
obs--94.91 %

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