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- PDB-1quu: CRYSTAL STRUCTURE OF TWO CENTRAL SPECTRIN-LIKE REPEATS FROM ALPHA... -

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Basic information

Entry
Database: PDB / ID: 1quu
TitleCRYSTAL STRUCTURE OF TWO CENTRAL SPECTRIN-LIKE REPEATS FROM ALPHA-ACTININ
ComponentsHUMAN SKELETAL MUSCLE ALPHA-ACTININ 2
KeywordsCONTRACTILE PROTEIN / TRIPLE-HELIX COILED COIL
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 / Striated Muscle Contraction / Assembly and cell surface presentation of NMDA receptors / cardiac muscle cell development / Nephrin family interactions / 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 / postsynaptic density, intracellular component / Long-term potentiation / negative regulation of potassium ion transport / titin binding / phosphatidylinositol-4,5-bisphosphate binding / regulation of membrane potential / cytoskeletal protein binding / Ras activation upon Ca2+ influx through NMDA receptor / 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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / 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 / Resolution: 2.5 Å
AuthorsDjinovic-Carugo, K. / Young, P. / Gautel, M. / Saraste, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structure of the alpha-actinin rod: molecular basis for cross-linking of actin filaments.
Authors: Djinovic-Carugo, K. / Young, P. / Gautel, M. / Saraste, M.
History
DepositionJul 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4May 30, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.5Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN SKELETAL MUSCLE ALPHA-ACTININ 2


Theoretical massNumber of molelcules
Total (without water)29,2841
Polymers29,2841
Non-polymers00
Water2,720151
1
A: HUMAN SKELETAL MUSCLE ALPHA-ACTININ 2

A: HUMAN SKELETAL MUSCLE ALPHA-ACTININ 2


Theoretical massNumber of molelcules
Total (without water)58,5682
Polymers58,5682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area2800 Å2
ΔGint-8 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.050, 60.050, 390.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein HUMAN SKELETAL MUSCLE ALPHA-ACTININ 2


Mass: 29283.828 Da / Num. of mol.: 1
Fragment: SPECTRIN-LIKE REPEATS 2 AND 3 - AMINO ACIDS 391 TO 637
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: SKELETAL MUSCLE / Plasmid: PET 8C / Production host: Escherichia coli (E. coli) / References: UniProt: P35609
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG 400 (FLUKA), 100 MM MGSO4, 100 MM HEPES OR TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
1150 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mMDTT1drop
426 %PEG4001reservoir
5100 mM1reservoirMgSO4
6100 mMHEPES1reservoircan be replaced by Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.947
DetectorType: OFF-LINE SCANNER / Detector: IMAGE PLATE / Date: Feb 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.947 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 21275 / Num. obs: 21275 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.339 / % possible all: 89.8
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→25 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3105 1083 -RANDOM
Rwork0.2285 ---
obs0.2285 12245 89.3 %-
all-13328 --
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 0 151 2185
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009748
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_deg1.27188
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 57.2 Å2

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