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- PDB-1hci: CRYSTAL STRUCTURE OF THE ROD DOMAIN OF ALPHA-ACTININ -

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Basic information

Entry
Database: PDB / ID: 1hci
TitleCRYSTAL STRUCTURE OF THE ROD DOMAIN OF ALPHA-ACTININ
ComponentsALPHA-ACTININ 2
KeywordsTRIPLE-HELIX COILED COIL / CONTRACTILE PROTEIN / MUSCLE / Z-LINE / ACTIN-BINDING 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 / positive regulation of cation channel activity / LIM domain binding / negative regulation of protein localization to cell surface ...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 / positive regulation of cation channel activity / LIM domain binding / negative regulation of protein localization to cell surface / microspike assembly / postsynaptic actin cytoskeleton / muscle cell development / positive regulation of potassium ion transport / focal adhesion assembly / Assembly and cell surface presentation of NMDA receptors / Striated Muscle Contraction / cardiac muscle cell development / Nephrin family interactions / sarcomere organization / structural constituent of muscle / cortical actin cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / postsynaptic density, intracellular component / negative regulation of potassium ion transport / Long-term potentiation / titin binding / phosphatidylinositol-4,5-bisphosphate binding / regulation of membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / cytoskeletal protein binding / nuclear receptor coactivator activity / platelet alpha granule lumen / filopodium / cell projection / actin filament / protein localization to plasma membrane / postsynaptic density membrane / Z disc / actin filament binding / integrin binding / Platelet degranulation / cell junction / 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
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYlanne, J. / Scheffzek, K. / Young, P. / Saraste, M.
CitationJournal: Structure / Year: 2001
Title: Crystal Structure of the Alpha-Actinin Rod Reveals an Extensive Torsional Twist
Authors: Ylanne, J. / Scheffzek, K. / Young, P. / Saraste, M.
History
DepositionMay 4, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,4232
Polymers112,4232
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.280, 103.280, 218.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 56211.324 Da / Num. of mol.: 2
Fragment: SPECTRIN-LIKE REPEATS 1,2,3, AND 4 - AMINO ACIDS 274 - 746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: SKELETAL MUSCLE / Plasmid: PET 8C / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35609
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPDB CONTAINS N-TERM GLY SER SER FROM THE VECTOR

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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 % sol: 80.3 %
Crystal growpH: 8.5 / Details: 0.9 M (NH4)2SO4, 0.1 M TRISHCL PH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-10 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMdithiothreitol1drop
40.9 Mammonium sulfate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 2, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→82.78 Å / Num. obs: 63392 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 2.45 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.78 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.28 / % possible all: 99
Reflection
*PLUS
Num. measured all: 155820
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QUU

1quu


Resolution: 2.8→82.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3989928.9 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKEHOOD USING AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.295 6335 10 %RANDOM
Rwork0.27 ---
obs0.27 63392 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.9267 Å2 / ksol: 0.367476 e/Å3
Displacement parametersBiso mean: 71.8 Å2
Baniso -1Baniso -2Baniso -3
1-16.57 Å217.48 Å20 Å2
2--16.57 Å20 Å2
3----33.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.8→82.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7884 0 0 16 7900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.468 1058 10 %
Rwork0.448 9522 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:WATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.27 / Rfactor Rwork: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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