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- PDB-1mb8: Crystal Structure of the actin binding domain of plectin -

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Basic information

Entry
Database: PDB / ID: 1mb8
TitleCrystal Structure of the actin binding domain of plectin
ComponentsPlectin
KeywordsSTRUCTURAL PROTEIN / CALPONIN HOMOLOGY DOMAIN / ACTIN BINDING DOMAIN / INTEGRIN BETA4 HEMIDESMOSOMES / CYTOSKELETON / EPIDERMOLYSIS BULLOSA
Function / homology
Function and homology information


protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / tight junction organization / Type I hemidesmosome assembly / skeletal myofibril assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / intermediate filament cytoskeleton organization ...protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / tight junction organization / Type I hemidesmosome assembly / skeletal myofibril assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / intermediate filament cytoskeleton organization / regulation of vascular permeability / dystroglycan binding / cellular response to hydrostatic pressure / fibroblast migration / T cell chemotaxis / costamere / 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 / Assembly of collagen fibrils and other multimeric structures / sarcomere organization / nucleus organization / keratinocyte development / transmission of nerve impulse / brush border / sarcoplasm / establishment of skin barrier / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / respiratory electron transport chain / mitochondrion organization / 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 / gene expression / mitochondrial outer membrane / cadherin binding / axon / focal adhesion / dendrite / perinuclear region of cytoplasm / RNA binding / extracellular exosome / plasma membrane / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
Authorsde Pereda, J.M.
CitationJournal: Structure / Year: 2003
Title: Structural and Functional Analysis of the Actin Binding Domain of Plectin Suggests Alternative Mechanisms for Binding to F-Actin and Integrin Beta4
Authors: Garcia-Alvarez, B. / Bobkov, A. / Sonnenberg, A. / de Pereda, J.M.
History
DepositionAug 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE AUTHOR INFORMED THAT THE HWRAE INSERTION HAS BEEN DESCRIBED IN MOUSE. AUTHOR ALSO INFORMED ...SEQUENCE AUTHOR INFORMED THAT THE HWRAE INSERTION HAS BEEN DESCRIBED IN MOUSE. AUTHOR ALSO INFORMED THAT RESIDUE ASN 149 IS CORRECT AND THAT THE CONFLICT ON THIS POSITION IS LIKELY DUE TO POLYMORPHISM.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plectin


Theoretical massNumber of molelcules
Total (without water)28,4451
Polymers28,4451
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.597, 79.283, 82.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Plectin / HD1


Mass: 28444.568 Da / Num. of mol.: 1 / Fragment: Residues 59-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15149
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.93 Å3/Da / Density % sol: 36.2 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MTris1reservoirpH7.0
215 %(v/v)2-propanol1reservoir
320 mg/mlprotein1drop
420 mMTris1droppH7.0
5150 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 24, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→35 Å / Num. all: 12571 / Num. obs: 11486 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.9 Å2
Reflection shellResolution: 2.15→2.28 Å / % possible all: 69.2
Reflection
*PLUS
Lowest resolution: 32 Å / % possible obs: 91.2 % / Num. measured all: 42883 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Lowest resolution: 2.23 Å / % possible obs: 61.4 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→31.11 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 862 7.5 %RANDOM
Rwork0.212 ---
all-12571 --
obs-11453 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2332 Å2 / ksol: 0.310086 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--0.7 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.15→31.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 0 153 2154
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it2.861.5
X-RAY DIFFRACTIONc_mcangle_it4.112
X-RAY DIFFRACTIONc_scbond_it2.952
X-RAY DIFFRACTIONc_scangle_it5.522.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 109 7.7 %
Rwork0.229 1314 -
obs-1423 69.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 32 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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