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- PDB-5dzz: Structural characterization of intermediate filaments binding dom... -

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Basic information

Entry
Database: PDB / ID: 5dzz
TitleStructural characterization of intermediate filaments binding domain of desmoplakin
ComponentsDesmoplakin
KeywordsSTRUCTURAL PROTEIN / desmoplakin / PRD / intermediate filaments
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsChoi, H.-J. / Weis, W.I.
CitationJournal: Plos One / Year: 2016
Title: Structure of the Intermediate Filament-Binding Region of Desmoplakin.
Authors: Kang, H. / Weiss, T.M. / Bang, I. / Weis, W.I. / Choi, H.J.
History
DepositionSep 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list / reflns_shell / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Desmoplakin


Theoretical massNumber of molelcules
Total (without water)54,5551
Polymers54,5551
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24470 Å2
Unit cell
Length a, b, c (Å)111.931, 64.466, 74.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Desmoplakin /


Mass: 54555.172 Da / Num. of mol.: 1 / Fragment: UNP residues 1960-2448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSP / Plasmid: pPROEX-HTb / Production host: Escherichia coli (E. coli) / References: UniProt: P15924
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 22% PEG MME 5000, magnesium acetate, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→74.044 Å / Num. obs: 18815 / % possible obs: 98 % / Redundancy: 2.9 % / Biso Wilson estimate: 37.58 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/av σ(I): 6.913 / Net I/σ(I): 10.6 / Num. measured all: 54886
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueNet I/σ(I) obs% possible all
2.6-2.730.3162.310206910.3162.493
2.77-2.8730.2762.4395913390.2764.498.1
2.87-2.9830.2053.3387912930.205698.6
2.98-3.13.10.1773.9380612470.1776.998.9
3.1-3.243.20.1454.8385412100.1459.199.2
3.24-3.393.20.1175.9370611590.11710.899.1
3.39-3.583.20.0996.9351810960.09912.799.4
3.58-3.793.20.0818.3339310460.08114.999.1
3.79-4.063.20.0689.631889850.06817.799.1
4.06-4.383.20.06110.229699200.06119.398.7
4.38-4.83.20.05610.926968500.05619.998.7
4.8-5.373.10.05611.124307850.05618.798.9
5.37-6.23.10.06110.620716720.06117.596.7
6.2-7.592.90.04612.816035520.04620.494.7
7.59-10.733.10.0414.615214880.0425.899.3
10.73-74.0442.80.04612.87582690.04626.696.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.0.15data scaling
Cootmodel building
PHENIXdev_1760refinement
PDB_EXTRACT3.15data extraction
SCALAdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LM7

1lm7


Resolution: 2.6→48.62 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 1319 7.92 %
Rwork0.207 15327 -
obs0.2115 16646 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.61 Å2 / Biso mean: 46.6793 Å2 / Biso min: 11.03 Å2
Refinement stepCycle: final / Resolution: 2.6→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 0 84 3884
Biso mean---33.29 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023852
X-RAY DIFFRACTIONf_angle_d0.5015195
X-RAY DIFFRACTIONf_chiral_restr0.02603
X-RAY DIFFRACTIONf_plane_restr0.002675
X-RAY DIFFRACTIONf_dihedral_angle_d9.811492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6002-2.70430.31141340.25991608174293
2.7043-2.82740.37961460.2771658180497
2.8274-2.97640.36331300.26491712184298
2.9764-3.16290.32111580.26511680183899
3.1629-3.4070.30281230.24541727185099
3.407-3.74980.28181790.21561678185799
3.7498-4.29210.22261520.17091734188699
4.2921-5.40640.2241280.16641768189698
5.4064-48.62890.19961690.16651762193195
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.88011.94830.7729.39032.82252.3559-0.10370.0923-0.2535-0.10340.2238-0.26970.06790.082-0.13460.23030.0603-0.02030.23550.01730.198516.4415-24.620912.699
22.95040.3667-0.18342.4160.44940.69830.0612-0.179-0.01260.11390.03030.0162-0.0349-0.0031-0.1090.30720.0360.02430.24960.01190.15316.9592-14.119817.7588
33.99565.85130.73125.75311.00740.1102-0.49830.366-0.0457-0.48250.3633-0.15950.01540.08950.13920.32090.0307-0.02280.28850.0240.469639.957110.461610.0574
44.93690.6229-0.39293.4676-0.20532.7563-0.02960.05950.01010.01830.15380.0446-0.1074-0.1646-0.11590.24460.0467-0.00940.12520.00330.223548.976735.236915.0296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1960 through 2055 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2056 through 2182 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2183 through 2273 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2274 through 2448 )A0

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