SASDDR4: LIM/homeobox protein Lhx4 LIM domains fused to the LIM interactio...

Basic information

• Entry: Database: SASBDB / ID: SASDDR4

Sample

LIM/homeobox protein Lhx4 LIM domains fused to the LIM interaction domain (LID) R282G mutant of Insulin gene enhancer protein ISL-2

• LIM/homeobox protein Lhx4 (protein), Lhx4-LIM domains, Mus musculus
• Insulin gene enhancer protein ISL-2 (R282G) (protein), ISL-2 (R282G), Mus musculus

Function / homology

Function:

visceral motor neuron differentiation / medial motor column neuron differentiation / spinal cord motor neuron cell fate specification / neuron fate specification / neuron fate commitment / methyl-CpG binding / motor neuron axon guidance / retinal ganglion cell axon guidance / negative regulation of neuron differentiation / cis-regulatory region sequence-specific DNA binding / axonogenesis / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / placenta development / neuron differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding

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 Lhx4 / Insulin gene enhancer protein ISL-2

• Biological species: Mus musculus (house mouse)
• Citation: Journal: Proteins / Year: 2019; Title: Mutation in a flexible linker modulates binding affinity for modular complexes.; Authors: Philippa H Stokes / Neil O Robertson / Ana P G Silva / Tanya Estephan / Jill Trewhella / J Mitchell Guss / Jacqueline M Matthews / ; Abstract: Tandem beta zippers are modular complexes formed between repeated linear motifs and tandemly arrayed domains of partner proteins in which β-strands form upon binding. Studies of such complexes, formed by LIM domain proteins and linear motifs in their intrinsically disordered partners, revealed spacer regions between the linear motifs that are relatively flexible but may affect the overall orientation of the binding modules. We demonstrate that mutation of a solvent exposed side chain in the spacer region of an LHX4-ISL2 complex has no significant effect on the structure of the complex, but decreases binding affinity, apparently by increasing flexibility of the linker.

Contact author

• Philippa Stokes (School of Life and Environmental Science, University of Sydney, Sydney, Australia)

Models

• Model #1595: ; Type: dummy / Radius of dummy atoms: 2.20 A; Comment: One of 20 models generated using DAMMIN that went into creating the Damfilt model.; Chi-square value: 4.442; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1596: ; Type: dummy / Radius of dummy atoms: 2.00 A; Comment: Damfilt model derived from multiple DAMMIN runs where 20 models were generated, spatially aligned.; Chi-square value: 4.442; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: LIM/homeobox protein Lhx4 LIM domains fused to the LIM interaction domain (LID) R282G mutant of Insulin gene enhancer protein ISL-2; Specimen concentration: 0.20-1.90 / Entity id: 814 / 816
• Buffer: Name: 20 mM Tris, 150 mM NaCl, 1 mM TCEP / pH: 8

Entity #814

Name: Lhx4-LIM domains / Type: protein / Description: LIM/homeobox protein Lhx4 / Formula weight: 14.712 / Num. of mol.: 1 / Source: Mus musculus / References: UniProt: P53776
Sequence:

GSMQQIPQCA GCNQHILDKF ILKVLDRHWH SSCLKCADCQ MQLADRCFSR AGSVYCKEDF FKRFGTKCTA CQQGIPPTQV VRKAQDFVYH LHCFACIICN RQLATGDEFY LMEDGRLVCK EDYETAKQ

Entity #816

Name: ISL-2 (R282G) / Type: protein / Description: Insulin gene enhancer protein ISL-2 (R282G) / Formula weight: 3.932 / Num. of mol.: 1 / Source: Mus musculus / References: UniProt: Q9CXV0
Sequence:

GGSGGHMGSG GGTPLVAGSP IGHENAVQGS AVEVQTYQPP W

Experimental information

• Beam: Instrument name: Australian Synchrotron SAXS/WAXS / City: Melbourne / 国: Australia / Shape: Point / Type of source: X-ray synchrotron / Wavelength: 0.10332 Å
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: LIM/homeobox protein Lhx4 LIM domains fused to the LIM interaction domain (LID) R282G mutant of Insulin gene enhancer protein ISL-2
Measurement date: Nov 19, 2015 / Cell temperature: 13.5 °C / Exposure time: 1 sec. / Number of frames: 24 / Unit: 1/A /

	Min	Max
Q	0.0064	0.3277

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 817 /

	Min	Max
Q	0.00956213	0.327682
P(R) point	1	817
R	0	84.69

Result

Type of curve: extrapolated
Comments: The protein anaysed is a fusion of two interacting partners: the LIM domains of Lhx4 and the LID of Isl2, with a point mutation within the Isl2-LID (R282G). The ab initio bead models presented in this entry include: 1) The best-fit individual reconstruction (top) and; 2) The spatially aligned and volume/bead occupancy-corrected averaged representation of the protein in solution (bottom) calculated from twenty individual reconstructions (NSD = 0.67; resolution estimate = 2.8 nm). Five concentrations of protein were subjected to SAXS as static samples (96-well plate) at the Australian Synchrotron. Subtle concentration dependent effects were noted. All data and additional information relating to the concentration series is included in the full-entry zip archive. The protein was subjected to SEC (off line) as the last purification step just prior to data collection. Also refer to the related SASBDB entry SASDDQ4.

	Experimental	Standard	Porod
MW	15 kDa	17 kDa	-
Volume	-	-	20.7 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.03409	5.0E-5	0.03394	4.0E-5
Radius of gyration, Rg	2.36 nm	0.005	2.27 nm	0.01

	Min	Max
D	-	8.47
Guinier point	10	131