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- PDB-5a38: Mutations in the Calponin homology domain of Alpha-Actinin-2 affe... -

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Basic information

Entry
Database: PDB / ID: 5a38
TitleMutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle.
ComponentsALPHA-ACTININ-2
KeywordsACTIN-BINDING PROTEIN / HUMAN ALPHA-ACTININ-2 / 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 / phosphatidylinositol-4,5-bisphosphate binding / titin binding / cytoskeletal protein binding / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / platelet alpha granule lumen / nuclear receptor coactivator activity / filopodium / cell projection / protein localization to plasma membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionMay 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,1742
Polymers57,1742
Non-polymers00
Water3,621201
1
A: ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)28,5871
Polymers28,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)28,5871
Polymers28,5871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.300, 46.560, 70.160
Angle α, β, γ (deg.)73.81, 80.26, 75.38
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28586.887 Da / Num. of mol.: 2 / Fragment: CALPONIN HOMOLOGY DOMAIN, RESIDUES 19 TO 266
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

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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: 40 % / Description: NONE
Crystal growpH: 7.5 / Details: 22% POLYETHYLENE GLYCOL 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9464
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2012 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9464 Å / Relative weight: 1
ReflectionResolution: 1.9→43.65 Å / Num. obs: 33050 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.1 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WKU

1wku


Resolution: 1.9→67 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.953 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23088 1659 5 %RANDOM
Rwork0.19182 ---
obs0.19377 31389 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.428 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0.2 Å20.42 Å2
2--0.72 Å20.14 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 0 201 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193691
X-RAY DIFFRACTIONr_bond_other_d0.0010.023627
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9554988
X-RAY DIFFRACTIONr_angle_other_deg0.95338352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9495452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17424.386171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31615697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3041524
X-RAY DIFFRACTIONr_chiral_restr0.0780.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024129
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02835
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_it0.8982.041799
X-RAY DIFFRACTIONr_mcbond_other0.8972.0391798
X-RAY DIFFRACTIONr_mcangle_it1.5963.0512251
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8612.1521892
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 121 -
Rwork0.281 2338 -
obs--93.71 %
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)
10.53740.0783-0.30510.2451-0.36211.2198-0.0022-0.0170.0156-0.01060.04580.013-0.06670.0674-0.04360.0123-0.01440.00530.05260.01110.01218.507852.775121.7465
20.6257-0.220.12520.2508-0.46661.1902-0.007-0.0267-0.026-0.00670.02640.03410.05840.0796-0.01930.0090.02490.0070.08250.03030.016211.129666.950552.904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 257
2X-RAY DIFFRACTION2B35 - 257

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