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- PDB-5a36: Mutations in the Calponin homology domain of Alpha-Actinin-2 affe... -

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Basic information

Entry
Database: PDB / ID: 5a36
TitleMutations in the Calponin homology domain of Alpha-Actinin-2 affect Actin binding and incorporation in muscle.
ComponentsALPHA-ACTININ-2
KeywordsSTRUCTURAL PROTEIN
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: 2 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 1.2May 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: ALPHA-ACTININ-2
B: ALPHA-ACTININ-2


Theoretical massNumber of molelcules
Total (without water)57,1742
Polymers57,1742
Non-polymers00
Water2,108117
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)38.658, 47.491, 70.299
Angle α, β, γ (deg.)80.78, 80.80, 76.50
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, UNP RESIDUES 19-266
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.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDOMAIN CONTAINING RESIDUES 19 TO 266

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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: 2.2 Å3/Da / Density % sol: 43 %
Description: ANISOTROPIC DIFFRACTION RESULTED IN APPROXIMATELY TWENTY PERCENT OF A SINGLE WEDGE OF DATA OF BEING VERY POOR DIFFRACTION QUALITY.
Crystal growpH: 7.5 / Details: 30% POLYETHYLENE GLYCOL 1500, 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: 2→68.8 Å / Num. obs: 31249 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→68.82 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 12.684 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. R AND FREER FACTOR VALUES ARE LOWER THAN EXPECTED FOR TWO ANGSTROM DATA. THIS IS MOST LIKELY DUE TO A WEDGE POOR OF ANISOTROPIC DIFFRACTED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. R AND FREER FACTOR VALUES ARE LOWER THAN EXPECTED FOR TWO ANGSTROM DATA. THIS IS MOST LIKELY DUE TO A WEDGE POOR OF ANISOTROPIC DIFFRACTED DATA BUT THE DENSITY LOOKS GOOD THROUGHOUT THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.26854 1579 5.1 %RANDOM
Rwork0.21712 ---
obs0.21979 29670 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.363 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0.24 Å20.26 Å2
2---1.41 Å20.03 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2→68.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 0 117 3840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193799
X-RAY DIFFRACTIONr_bond_other_d0.0010.023719
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9575132
X-RAY DIFFRACTIONr_angle_other_deg0.84438559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64124.407177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46715711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5911525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
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_it1.2041.9211850
X-RAY DIFFRACTIONr_mcbond_other1.2021.921849
X-RAY DIFFRACTIONr_mcangle_it1.9682.8742309
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4812.1321949
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: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 99 -
Rwork0.299 1882 -
obs--82.03 %
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)
10.8303-0.2419-0.06150.9413-0.66440.7777-0.005-0.00150.0385-0.0282-0.0391-0.01220.02560.04490.04420.02940.01320.00180.15640.05820.03112.23959.3162.59
20.69540.4818-0.30040.6812-0.91361.9868-0.0357-0.0510.01120.0217-0.0375-0.0075-0.06970.04530.07320.03650.0173-0.00170.15060.04820.021919.17347.78529.02
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 257
2X-RAY DIFFRACTION2B33 - 256

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