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- PDB-1sh6: Crystal structure of actin-binding domain of mouse plectin -

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Basic information

Entry
Database: PDB / ID: 1sh6
TitleCrystal structure of actin-binding domain of mouse plectin
ComponentsPlectin 1
KeywordsSTRUCTURAL PROTEIN / plectin / actin-binding domain / calponin-homology domain
Function / homology
Function and homology information


Type I hemidesmosome assembly / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / Caspase-mediated cleavage of cytoskeletal proteins / skeletal myofibril assembly / tight junction organization / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / contractile muscle fiber ...Type I hemidesmosome assembly / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / Caspase-mediated cleavage of cytoskeletal proteins / skeletal myofibril assembly / tight junction organization / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / contractile muscle fiber / intermediate filament organization / : / regulation of vascular permeability / intermediate filament cytoskeleton organization / dystroglycan binding / cellular response to hydrostatic pressure / fibroblast migration / myelination in peripheral nervous system / T cell chemotaxis / cellular response to fluid shear stress / peripheral nervous system myelin maintenance / cardiac muscle cell development / myoblast differentiation / adherens junction organization / intermediate filament / response to food / structural constituent of muscle / ankyrin binding / skin development / sarcomere organization / myofibril / nucleus organization / keratinocyte development / transmission of nerve impulse / brush border / sarcoplasm / establishment of skin barrier / skeletal muscle fiber development / skeletal muscle tissue development / keratinocyte differentiation / respiratory electron transport chain / cytoskeletal protein binding / mitochondrion organization / response to nutrient / basal plasma membrane / cell periphery / cell motility / actin filament organization / wound healing / protein localization / cell morphogenesis / multicellular organism growth / structural constituent of cytoskeleton / sarcolemma / Z disc / cellular response to mechanical stimulus / : / actin filament binding / myelin sheath / actin binding / gene expression / actin cytoskeleton organization / mitochondrial outer membrane / cadherin binding / apical plasma membrane / axon / focal adhesion / dendrite / perinuclear region of cytoplasm / cytosol / cytoplasm
Similarity search - Function
: / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain ...: / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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. / Plectin/S10, N-terminal / Plectin/S10 domain / Src homology 3 (SH3) domain profile. / SH3 domain / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSevcik, J. / Urbanikova, L.
Citation
Journal: Eur.J.Biochem. / Year: 2004
Title: Actin-binding domain of mouse plectin: crystal structure and binding to vimentin
Authors: Sevcik, J. / Urbanikova, L. / Kostan, J. / Janda, L. / Wiche, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Purification, crystallization and preliminary X-ray analysis of the plectin actin-binding domain
Authors: Urbanikova, L. / Janda, L. / Popov, A. / Wiche, G. / Sevcik, J.
History
DepositionFeb 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plectin 1


Theoretical massNumber of molelcules
Total (without water)28,7181
Polymers28,7181
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.517, 51.226, 144.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Plectin 1 / / PLTN / PCN / plectin isoform plec 1 / 2alpha


Mass: 28717.717 Da / Num. of mol.: 1 / Fragment: actin-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pBN120 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9QXS1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.22 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, cacodylate, calcium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.812 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2003 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 17114 / Num. obs: 17114 / % possible obs: 97.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 33.9
Reflection shellResolution: 2→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.5 / Num. unique all: 498 / % possible all: 86.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.893 / SU B: 5.103 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29956 848 5.1 %RANDOM
Rwork0.19755 ---
all0.202 17114 --
obs0.20238 15889 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.572 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--0.88 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 0 174 3948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0211921
X-RAY DIFFRACTIONr_bond_other_d0.0030.021754
X-RAY DIFFRACTIONr_angle_refined_deg2.5941.9442597
X-RAY DIFFRACTIONr_angle_other_deg1.27634073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7055229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.210.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022113
X-RAY DIFFRACTIONr_gen_planes_other0.0210.02387
X-RAY DIFFRACTIONr_nbd_refined0.250.2511
X-RAY DIFFRACTIONr_nbd_other0.2670.22181
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1140.21216
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.3851.51146
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.57321856
X-RAY DIFFRACTIONr_scbond_it5.2683775
X-RAY DIFFRACTIONr_scangle_it7.2644.5741
X-RAY DIFFRACTIONr_rigid_bond_restr2.77521921
X-RAY DIFFRACTIONr_sphericity_free17.96558
X-RAY DIFFRACTIONr_sphericity_bonded6.45851884
LS refinement shellResolution: 2→2.02 Å / Rfactor Rfree error: 0.21 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 59 -
Rwork0.211 1048 -
obs-848 86.3 %

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