SASDAT6: Integrin beta4, fragment of the cytoplasmic region encompassing t...

Basic information

• Entry: Database: SASBDB / ID: SASDAT6

Sample

Integrin beta4, fragment of the cytoplasmic region encompassing the third and fourth FnIII domains

• Integrin beta-4 (protein), Homo sapiens

Function / homology

Function:

trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation / integrin complex / Assembly of collagen fibrils and other multimeric structures / cell adhesion mediated by integrin / Syndecan interactions / cell leading edge / basement membrane / cell-matrix adhesion / basal plasma membrane / integrin-mediated signaling pathway / G protein-coupled receptor binding / cell motility / autophagy / cell-cell adhesion / response to wounding / integrin binding / cell junction / nuclear membrane / receptor complex / cell adhesion / focal adhesion / nucleolus / cell surface / extracellular exosome / metal ion binding / plasma membrane

Domain/homology:

Integrin beta-4 subunit / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold

Component:

Integrin beta-4

• Biological species: Homo sapiens (human)
• Citation: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2015; Title: Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4.; Authors: Noelia Alonso-García / Inés García-Rubio / José A Manso / Rubén M Buey / Hector Urien / Arnoud Sonnenberg / Gunnar Jeschke / José M de Pereda / ; Abstract: Integrin α6β4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6β4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3,4) of integrin β4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron-electron resonance (DEER) complement each other to solve the structure of the FnIII-3,4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3,4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes.

Contact author

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

Models

• Model #219: ; Type: dummy / Software: DAMMIF / Radius of dummy atoms: 1.50 A / Chi-square value: 1.976836; Search similar-shape structures of this assembly by Omokage search (details)
• Model #220: ; Type: atomic / Software: CRYSOL / Chi-square value: 1.297321; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Integrin beta4, fragment of the cytoplasmic region encompassing the third and fourth FnIII domains; Specimen concentration: 1.50-48.60
• Buffer: Name: Sodium Phosphate / Concentration: 20.00 mM / pH: 7.5 / Composition: 150 mM NaCl, 5% glycerol, 3 mM DTT

Entity #133

Type: protein / Description: Integrin beta-4 / Formula weight: 23.359 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P16144
Sequence:

GSHMVPDTPT RLVFSALGPT SLRVSWQEPR CERPLQGYSV EYQLLNGGEL HRLNIPNPAQ TSVVVEDLLP NHSYVFRVRA QSQEGWGRER EGVITIESQV HPQSPLCPLP GSAFTLSTPS APGPLVFTAL SPDSLQLSWE RPRRPNGDIV GYLVTCEMAQ GGGPATAFRV DGDSPESRLT VPGLSENVPY KFKVQARTTE GFGPEREGII TIES

Experimental information

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

Scan

Measurement date: Aug 6, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0576	3.4909

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 494 /

	Min	Max
Q	0.05955	3.013
P(R) point	1	494
R	0	7

Result

D max: 7 / Type of curve: extrapolated
Comments: Combined use of SAXS, crystal structures, site directed spin labeling, double electron-electron resonance (DEER), and molecular modeling to analyze the structure of FnIII-3,4.

	Experimental	Standard	Porod
MW	19.2 kDa	19.2 kDa	20 kDa
Volume	-	-	32 nm3

	P(R)	Guinier
Forward scattering, I0	586	590
Radius of gyration, Rg	2.2 nm	2.2 nm