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- PDB-1lm5: Structures of two intermediate filament-binding fragments of desm... -

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Basic information

Entry
Database: PDB / ID: 1lm5
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 / intermediate filament organization / epithelial cell-cell adhesion / intermediate filament cytoskeleton organization / desmosome ...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 / intermediate filament organization / epithelial cell-cell adhesion / intermediate filament cytoskeleton organization / desmosome / 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 / intermediate filament / skin development / regulation of heart rate by cardiac conduction / ficolin-1-rich granule membrane / intercalated disc / epidermis development / keratinocyte differentiation / adherens junction / protein kinase C binding / 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 / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Spectrin-like repeat ...beta-hairpin-alpha-hairpin repeat / Plakin 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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)46,5992
Polymers46,5992
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.320, 95.379, 54.982
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 subdomain of Desmoplakin Carboxy-Terminal domain (DPCT)


Mass: 23299.523 Da / Num. of mol.: 2 / Fragment: residues 2609-2822
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1.92 Å3/Da / Density % sol: 35.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 4000, magnesium chloride, acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
2100 mMsodium acetate1reservoirpH5.2
331 %(w/v)PEG40001reservoir
4150 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.925 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.925 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 32732 / Num. obs: 31807 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.3 Å2 / Rsym value: 0.031
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.297 / % possible all: 90.3
Reflection
*PLUS
Lowest resolution: 45 Å / Num. obs: 32732 / Num. measured all: 292583 / Rmerge(I) obs: 0.031
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 90.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→32.16 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 746377.97 / Data cutoff high rms absF: 746377.97 / 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
Rfree0.247 2572 8.1 %RANDOM
Rwork0.203 ---
obs0.203 31807 93.4 %-
all-32732 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8859 Å2 / ksol: 0.348658 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.15 Å20 Å20 Å2
2--5.99 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→32.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 0 284 3212
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.332
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 361 7.9 %
Rwork0.252 4229 -
obs--82.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 45 Å / % reflection Rfree: 8 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.313 / Rfactor Rwork: 0.252

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