SASDBE4: Plakin domain of Human desmoplakin (Plakin domain of Human Desmop...

Basic information

• Entry: Database: SASBDB / ID: SASDBE4

Sample

Plakin domain of Human desmoplakin

• Plakin domain of Human Desmoplakin (protein), Desmoplakin, Homo sapiens

Function / homology

Function:

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

Domain/homology:

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

Component:

Desmoplakin

• Biological species: Homo sapiens (human)
• Citation: Journal: J Biol Chem / Year: 2016; Title: The Structure of the Plakin Domain of Plectin Reveals an Extended Rod-like Shape.; Authors: Esther Ortega / José A Manso / Rubén M Buey / Ana M Carballido / Arturo Carabias / Arnoud Sonnenberg / José M de Pereda / ; Abstract: Plakins are large multi-domain proteins that interconnect cytoskeletal structures. Plectin is a prototypical plakin that tethers intermediate filaments to membrane-associated complexes. Most plakins contain a plakin domain formed by up to nine spectrin repeats (SR1-SR9) and an SH3 domain. The plakin domains of plectin and other plakins harbor binding sites for junctional proteins. We have combined x-ray crystallography with small angle x-ray scattering (SAXS) to elucidate the structure of the plakin domain of plectin, extending our previous analysis of the SR1 to SR5 region. Two crystal structures of the SR5-SR6 region allowed us to characterize its uniquely wide inter-repeat conformational variability. We also report the crystal structures of the SR7-SR8 region, refined to 1.8 Å, and the SR7-SR9 at lower resolution. The SR7-SR9 region, which is conserved in all other plakin domains, forms a rigid segment stabilized by uniquely extensive inter-repeat contacts mediated by unusually long helices in SR8 and SR9. Using SAXS we show that in solution the SR3-SR6 and SR7-SR9 regions are rod-like segments and that SR3-SR9 of plectin has an extended shape with a small central kink. Other plakins, such as bullous pemphigoid antigen 1 and microtubule and actin cross-linking factor 1, are likely to have similar extended plakin domains. In contrast, desmoplakin has a two-segment structure with a central flexible hinge. The continuous versus segmented structures of the plakin domains of plectin and desmoplakin give insight into how different plakins might respond to tension and transmit mechanical signals.

Contact author

• Jose M de Pereda (USAL, La Universidad de Salamanca, Salamanca, Spain)

Models

• Model #505: ; Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.192 / P-value: 0.000004; Search similar-shape structures of this assembly by Omokage search (details)
• Model #506: ; Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.192 / P-value: 0.000004; Search similar-shape structures of this assembly by Omokage search (details)
• Model #507: ; Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.192 / P-value: 0.000004; Search similar-shape structures of this assembly by Omokage search (details)
• Model #508: ; Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.192 / P-value: 0.000004; Search similar-shape structures of this assembly by Omokage search (details)
• Model #509: ; Type: mix / Software: EOM / Radius of dummy atoms: 1.90 A / Chi-square value: 3.192 / P-value: 0.000004; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Plakin domain of Human desmoplakin / Specimen concentration: 0.59-4.70
• Buffer: Name: sodium phosphate / Concentration: 20.00 mM / pH: 7.5 / Composition: 150 mM NaCl, 5% glycerol, 3 mM DTT

Entity #323

Name: Desmoplakin / Type: protein / Description: Plakin domain of Human Desmoplakin / Formula weight: 98.68 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P15924
Sequence:

GSHMWDEFTK HVTSECLGWM RQQRAEMDMV AWGVDLASVE QHINSHRGIH NSIGDYRWQL DKIKADLREK SAIYQLEEEY ENLLKASFER MDHLRQLQNI IQATSREIMW INDCEEEELL YDWSDKNTNI AQKQEAFSIR MSQLEVKEKE LNKLKQESDQ LVLNQHPASD KIEAYMDTLQ TQWSWILQIT KCIDVHLKEN AAYFQFFEEA QSTEAYLKGL QDSIRKKYPC DKNMPLQHLL EQIKELEKER EKILEYKRQV QNLVNKSKKI VQLKPRNPDY RSNKPIILRA LCDYKQDQKI VHKGDECILK DNNERSKWYV TGPGGVDMLV PSVGLIIPPP NPLAVDLSCK IEQYYEAILA LWNQLYINMK SLVSWHYCMI DIEKIRAMTI AKLKTMRQED YMKTIADLEL HYQEFIRNSQ GSEMFGDDDK RKIQSQFTDA QKHYQTLVIQ LPGYPQHQTV TTTEITHHGT CQDVNHNKVI ETNRENDKQE TWMLMELQKI RRQIEHCEGR MTLKNLPLAD QGSSHHITVK INELKSVQND SQAIAEVLNQ LKDMLANFRG SEKYCYLQNE VFGLFQKLEN INGVTDGYLN SLCTVRALLQ AILQTEDMLK VYEARLTEEE TVCLDLDKVE AYRCGLKKIK NDLNLKKSLL ATMKTELQKA QQIHSQTSQQ YPLYDLDLGK FGEKVTQLTD RWQRIDKQID FRLWDLEKQI KQLRNYRDNY QAFCKWLYDA KRRQDSLESM KFGDSNTVMR FLNEQKNLHS EISGKRDKSE EVQKIAELCA NSIKDYELQL ASYTSGLETL LNIPIKRTMI QSPSGVILQE AADVHARYIE LLTRSGDYYR

Experimental information

• Beam: Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Plakin domain of Human desmoplakin / Measurement date: Sep 25, 2015 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 30 / Unit: 1/nm /

	Min	Max
Q	0.0622	4.8124

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1120 /

	Min	Max
Q	0.0622081	3.02016
P(R) point	1	1120
R	0	35

Result

D max: 35 / Type of curve: extrapolated
Comments: The models displayed for this entry are selected representatives from a refined ensemble of conformations derived from ensemble optimization method (EOM). The Rg and Dmax distributions of the ensemble and the additional results from EOM (that includes additional structural representatives) are available in the full-entry zip archive. The corresponding fit for this entry shows the final EOM fit to the SAXS data of the total refined ensemble.

	Experimental	Porod
MW	114 kDa	85 kDa
Volume	-	136 nm3

	P(R)	Guinier
Forward scattering, I0	25920	25300
Radius of gyration, Rg	8.34 nm	7.49 nm