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- PDB-1sh5: Crystal structure of actin-binding domain of mouse plectin -

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Basic information

Entry
Database: PDB / ID: 1sh5
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 / leukocyte migration involved in immune response / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / Caspase-mediated cleavage of cytoskeletal proteins / tight junction organization / skeletal myofibril assembly / hemidesmosome assembly / hemidesmosome / contractile muscle fiber ...Type I hemidesmosome assembly / leukocyte migration involved in immune response / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / Caspase-mediated cleavage of cytoskeletal proteins / tight junction organization / skeletal myofibril assembly / hemidesmosome assembly / hemidesmosome / contractile muscle fiber / intermediate filament organization / intermediate filament cytoskeleton organization / regulation of vascular permeability / 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 / adherens junction organization / cardiac muscle cell development / myoblast differentiation / podosome / intermediate filament cytoskeleton / response to food / structural constituent of muscle / ankyrin binding / sarcomere organization / skin development / 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 / cytoskeletal protein binding / respiratory electron transport chain / response to nutrient / basal plasma membrane / actin filament organization / cell periphery / mitochondrion organization / cell motility / wound healing / cell morphogenesis / multicellular organism growth / sarcolemma / structural constituent of cytoskeleton / Z disc / cellular response to mechanical stimulus / actin filament binding / protein localization / myelin sheath / actin binding / gene expression / actin cytoskeleton organization / mitochondrial outer membrane / apical plasma membrane / axon / focal adhesion / dendrite / perinuclear region of cytoplasm / cytosol / cytoplasm
Similarity search - Function
Spectrin repeat / : / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain ...Spectrin repeat / : / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Spectrin-like repeat / Plectin repeat / Plakin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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. / 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 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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
B: Plectin 1


Theoretical massNumber of molelcules
Total (without water)57,4352
Polymers57,4352
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.310, 108.920, 63.750
Angle α, β, γ (deg.)90.00, 115.25, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

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


Mass: 28717.717 Da / Num. of mol.: 2 / 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


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.08 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 16, 2000 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 49742 / Num. obs: 47802 / % possible obs: 96.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.2
Reflection shellResolution: 1.95→1.97 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1187 / % possible all: 71.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAG

1qag


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.892 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19422 2286 5.1 %RANDOM
Rwork0.15103 ---
all0.1532 46097 --
obs0.15314 42818 97.88 %-
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: 39.942 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å22.47 Å2
2---2.62 Å20 Å2
3---2.54 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7688 0 0 564 8252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0213914
X-RAY DIFFRACTIONr_bond_other_d0.0020.023574
X-RAY DIFFRACTIONr_angle_refined_deg2.021.9425286
X-RAY DIFFRACTIONr_angle_other_deg1.04938300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5375462
X-RAY DIFFRACTIONr_chiral_restr0.2230.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024304
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02804
X-RAY DIFFRACTIONr_nbd_refined0.2390.2861
X-RAY DIFFRACTIONr_nbd_other0.2490.24125
X-RAY DIFFRACTIONr_nbtor_other0.0980.22479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3820.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.211
X-RAY DIFFRACTIONr_mcbond_it2.1561.52312
X-RAY DIFFRACTIONr_mcangle_it3.44123750
X-RAY DIFFRACTIONr_scbond_it4.74931602
X-RAY DIFFRACTIONr_scangle_it7.2274.51536
X-RAY DIFFRACTIONr_rigid_bond_restr2.35423914
X-RAY DIFFRACTIONr_sphericity_free18.6385188
X-RAY DIFFRACTIONr_sphericity_bonded6.1753838
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 137 -
Rwork0.199 2783 -
obs-1187 71.7 %

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