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- PDB-6cme: Structure of wild-type ISL2-LID in complex with LHX4-LIM1+2 -

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Basic information

Entry
Database: PDB / ID: 6cme
TitleStructure of wild-type ISL2-LID in complex with LHX4-LIM1+2
ComponentsLIM/homeobox protein Lhx4,Insulin gene enhancer protein ISL-2
KeywordsTRANSCRIPTION / LIM-homeodomain / cell-type specification / neural development
Function / homology
Function and homology information


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 ...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 / placenta development / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
: / : / : / : / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...: / : / : / : / Cysteine Rich Protein / Cysteine Rich Protein / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
LIM/homeobox protein Lhx4 / Insulin gene enhancer protein ISL-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsStokes, P.H. / Silva, A. / Guss, J.M. / Matthews, J.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140102318 Australia
CitationJournal: 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, ...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.
History
DepositionMar 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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: LIM/homeobox protein Lhx4,Insulin gene enhancer protein ISL-2
B: LIM/homeobox protein Lhx4,Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,02210
Polymers37,4992
Non-polymers5238
Water3,783210
1
A: LIM/homeobox protein Lhx4,Insulin gene enhancer protein ISL-2
hetero molecules


  • defined by author&software
  • Evidence: SAXS, Light scattering and SAXS data indicate that the molecule is monomeric ion solution. SAXS data indicates a more elongated structure indicating that the extreme bend in the structure ...Evidence: SAXS, Light scattering and SAXS data indicate that the molecule is monomeric ion solution. SAXS data indicates a more elongated structure indicating that the extreme bend in the structure is a crystallization artefact
  • 19 kDa, 1 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)19,0115
Polymers18,7491
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIM/homeobox protein Lhx4,Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0115
Polymers18,7491
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.488, 88.843, 50.303
Angle α, β, γ (deg.)90.00, 111.33, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe authors state that light scattering and SAXS data indicate that the molecule is monomeric ion solution. SAXS data indicates a more elongated structure indicating that the extreme bend in the structure is a crystallization artifact.

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Components

#1: Protein LIM/homeobox protein Lhx4,Insulin gene enhancer protein ISL-2 / LIM homeobox protein 4 / Islet-2


Mass: 18749.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lhx4, Gsh-4, Gsh4, Isl2 / Details (production host): pGEX-2T / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53776, UniProt: Q9CXV0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 53.34 % / Description: wedge-like thin sheets
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 110 mM BisTris propane and 3 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 2014
RadiationMonochromator: CONFOCAL MAXFLUX MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→27.55 Å / Num. obs: 29762 / % possible obs: 99.8 % / Redundancy: 4.6 % / Biso Wilson estimate: 23.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.063 / Rrim(I) all: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1441 / CC1/2: 0.393 / Rpim(I) all: 0.481 / Rrim(I) all: 0.915 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-20001.99.2data reduction
Aimless0.2.14data scaling
MOLREP11.2.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mmk

3mmk


Resolution: 1.92→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.568 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.147 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24343 1495 5.1 %RANDOM
Rwork0.20095 ---
obs0.20313 28066 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0 Å2-0.69 Å2
2---1.53 Å20 Å2
3---1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.92→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 8 210 2650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0142512
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172185
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.6573392
X-RAY DIFFRACTIONr_angle_other_deg0.8251.6415144
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87822.374139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70315425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7191516
X-RAY DIFFRACTIONr_chiral_restr0.0550.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02478
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8522.9541239
X-RAY DIFFRACTIONr_mcbond_other1.8492.9531238
X-RAY DIFFRACTIONr_mcangle_it3.044.4111543
X-RAY DIFFRACTIONr_mcangle_other3.044.4131544
X-RAY DIFFRACTIONr_scbond_it2.333.3281273
X-RAY DIFFRACTIONr_scbond_other2.3293.3271273
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8484.871848
X-RAY DIFFRACTIONr_long_range_B_refined5.84834.6582733
X-RAY DIFFRACTIONr_long_range_B_other5.78134.3362685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 104 -
Rwork0.338 2064 -
obs--97.92 %

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