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- PDB-1lm7: Structures of two intermediate filament-binding fragments of desm... -

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Basic information

Entry
Database: PDB / ID: 1lm7
TitleStructures of two intermediate filament-binding fragments of desmoplakin reveal a unique repeat motif structure
Componentssubdomain of Desmoplakin Carboxy-Terminal domain (DPCT)
KeywordsSTRUCTURAL PROTEIN / plakin repeat
Function / homology
Function and homology information


bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / protein localization to cell-cell junction / ventricular compact myocardium morphogenesis / desmosome / intermediate filament organization / epithelial cell-cell adhesion / intermediate filament cytoskeleton organization ...bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / protein localization to cell-cell junction / ventricular compact myocardium morphogenesis / desmosome / intermediate filament organization / epithelial cell-cell adhesion / intermediate filament cytoskeleton organization / Formation of the cornified envelope / peptide cross-linking / fascia adherens / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins / adherens junction organization / RND1 GTPase cycle / RND3 GTPase cycle / skin development / intermediate filament / regulation of heart rate by cardiac conduction / ficolin-1-rich granule membrane / intercalated disc / epidermis development / keratinocyte differentiation / protein kinase C binding / adherens junction / wound healing / structural constituent of cytoskeleton / cell-cell adhesion / scaffold protein binding / basolateral plasma membrane / Neutrophil degranulation / structural molecule activity / RNA binding / extracellular exosome / nucleus / plasma membrane / cytoplasm
Similarity search - Function
beta-hairpin-alpha-hairpin repeat / Plakin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain ...beta-hairpin-alpha-hairpin repeat / Plakin 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 / Spectrin/alpha-actinin / Spectrin repeats / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsChoi, H.J. / Park-Snyder, S. / Pascoe, L.T. / Green, K.J. / Weis, W.I.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structures of two intermediate filament-binding fragments of desmoplakin reveal a unique repeat motif structure.
Authors: Choi, H.J. / Park-Snyder, S. / Pascoe, L.T. / Green, K.J. / Weis, W.I.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: subdomain of Desmoplakin Carboxy-Terminal domain (DPCT)
B: subdomain of Desmoplakin Carboxy-Terminal domain (DPCT)


Theoretical massNumber of molelcules
Total (without water)55,1392
Polymers55,1392
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.293, 99.773, 51.687
Angle α, β, γ (deg.)90.00, 97.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein subdomain of Desmoplakin Carboxy-Terminal domain (DPCT)


Mass: 27569.258 Da / Num. of mol.: 2 / Fragment: residues 2209-2456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPROEX HTc / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P15924

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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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG1500, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
2100 mMMES1reservoirpH6.0
335 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 2001 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 11017 / Num. obs: 10670 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.088
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.232 / % possible all: 84.3
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. obs: 9183 / Num. measured all: 208172 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 84.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 15.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 3→35.74 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 322205.39 / Data cutoff high rms absF: 322205.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 916 10.2 %RANDOM
Rwork0.249 ---
obs0.249 8969 91.8 %-
all-9183 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.4838 Å2 / ksol: 0.301884 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1--11.78 Å20 Å22.84 Å2
2--13.75 Å20 Å2
3----1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 0 0 3708
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.831.5
X-RAY DIFFRACTIONc_mcangle_it3.142
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_scangle_it4.142.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 106 8.3 %
Rwork0.307 1174 -
obs--80 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 100 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.095
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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