SASDC22: Tandem LIM domains of the neuronal transcription factor homeobox ...

Basic information

• Entry: Database: SASBDB / ID: SASDC22

Sample

Tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7

• Homeobox protein CEH-14 (protein), CEH-14, Caenorhabditis elegans
• CeLIM-7 (protein), CeLIM-7, Caenorhabditis elegans

Function / homology

Function:

pharynx development / excretion / gonad morphogenesis / body morphogenesis / nematode larval development / thermosensory behavior / neuron fate specification / head morphogenesis / locomotion / neuron development / cis-regulatory region sequence-specific DNA binding / axonogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus

Domain/homology:

LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily

Component:

LIM/homeobox protein lim-7 / LIM/homeobox protein ceh-14

• Biological species: Caenorhabditis elegans (invertebrata)
• Citation: Journal: Sci Rep / Year: 2017; Title: Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans.; Authors: Mugdha Bhati / Estelle Llamosas / David A Jacques / Cy M Jeffries / Siavoush Dastmalchi / Nina Ripin / Hannah R Nicholas / Jacqueline M Matthews / ; Abstract: LIM-Homeodomain (LIM-HD) transcription factors are highly conserved in animals where they are thought to act in a transcriptional 'LIM code' that specifies cell types, particularly in the central nervous system. In chick and mammals the interaction between two LIM-HD proteins, LHX3 and Islet1 (ISL1), is essential for the development of motor neurons. Using yeast two-hybrid analysis we showed that the Caenorhabditis elegans orthologs of LHX3 and ISL1, CEH-14 and LIM-7 can physically interact. Structural characterisation of a complex comprising the LIM domains from CEH-14 and a LIM-interaction domain from LIM-7 showed that these nematode proteins assemble to form a structure that closely resembles that of their vertebrate counterparts. However, mutagenic analysis across the interface indicates some differences in the mechanisms of binding. We also demonstrate, using fluorescent reporter constructs, that the two C. elegans proteins are co-expressed in a small subset of neurons. These data show that the propensity for LHX3 and Islet proteins to interact is conserved from C. elegans to mammals, raising the possibility that orthologous cell specific LIM-HD-containing transcription factor complexes play similar roles in the development of neuronal cells across diverse species.

Contact author

• Cy M Jeffries (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #1139: ; Type: dummy / Radius of dummy atoms: 2.25 A / Chi-square value: 0.288 / P-value: 0.190200; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1140: ; Type: dummy / Radius of dummy atoms: 2.25 A / Chi-square value: 0.288 / P-value: 0.190200; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1141: ; Type: dummy / Radius of dummy atoms: 1.90 A / Chi-square value: 0.29 / P-value: 0.025700; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1142: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 0.295 / P-value: 0.192000; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7; Specimen concentration: 5.2 mg/ml / Entity id: 593 / 594
• Buffer: Name: 50 mM Tris, 100 mM NaCl, 5 mM TCEP, / pH: 8

Entity #593

Name: CEH-14 / Type: protein / Description: Homeobox protein CEH-14 / Formula weight: 15.693 / Num. of mol.: 1 / Source: Caenorhabditis elegans / References: UniProt: P20271
Sequence:

GSNNEEAICS LCDKKIRDRF VSKVNGRCYH SSCLRCSTCK DELGATCFLR EDSMYCRAHF YKKFGTKCSS CNEGIVPDHV VRKASNHVYH VECFQCFICK RSLETGEEFY LIADDARLVC KDDYEQARDG GSGGHMGSGG

Entity #594

Name: CeLIM-7 / Type: protein / Description: CeLIM-7 / Formula weight: 3.501 / Num. of mol.: 1 / Source: Caenorhabditis elegans / References: UniProt: G5EC36
Sequence:

GIGPLMVQPA TPHIDNTLGG PIDIQHFAQW EF

Experimental information

• Beam: Instrument name: University of Sydney Anton Paar SAXSess / City: Sydney / 国: Australia / Shape: Line collimation / Type of source: X-ray in house / Wavelength: 0.1542 Å / Dist. spec. to detc.: 0.309 mm
• Detector: Name: Roper Scientific PI-SCX:4300 / Type: KAF 2084 x 2084 SCX CCD / Pixsize x: 24 mm

Scan

Title: Tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7
Measurement date: Apr 7, 2009 / Cell temperature: 10 °C / Exposure time: 900 sec. / Number of frames: 4 / Unit: 1/nm /

	Min	Max
Q	0.0674	3.3112

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 439 /

	Min	Max
Q	0.067406	3.31124
P(R) point	1	439
R	0	8.9

Result

Type of curve: single_conc
Comments: The SAXS data displayed for this entry includes the beam-geometry corrected scattering profile (desmeared data, top, and homology model fit) as well as the fit of the ab initio models to the smeared SAXS data (i.e., smeared model-data fits). The original smeared data, prepared experimental beam profile and all individual DAMMIF and Gasbor models are included in the full entry zip archive.

	Experimental	Standard	Standard error	Porod
MW	17 kDa	16.7 kDa	0.9	16 kDa
Volume	-	-	-	25.6 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.0833	0.002	0.083	0.0002
Radius of gyration, Rg	2.51 nm	0.09	2.4 nm	0.03

	Min	Max
D	-	8.9
Guinier point	1	61