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- PDB-2rgt: Crystal Structure of Lhx3 LIM domains 1 and 2 with the binding do... -

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Basic information

Entry
Database: PDB / ID: 2rgt
TitleCrystal Structure of Lhx3 LIM domains 1 and 2 with the binding domain of Isl1
ComponentsFusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1
KeywordsMETAL BINDING PROTEIN / protein-protein complex / LIM domain / Zn finger / Activator / DNA-binding / Homeobox / Metal-binding / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


sensory system development / positive regulation of macrophage colony-stimulating factor production / sinoatrial node cell development / prolactin secreting cell differentiation / trigeminal nerve development / peripheral nervous system neuron axonogenesis / somatotropin secreting cell differentiation / visceral motor neuron differentiation / medial motor column neuron differentiation / positive regulation of granulocyte colony-stimulating factor production ...sensory system development / positive regulation of macrophage colony-stimulating factor production / sinoatrial node cell development / prolactin secreting cell differentiation / trigeminal nerve development / peripheral nervous system neuron axonogenesis / somatotropin secreting cell differentiation / visceral motor neuron differentiation / medial motor column neuron differentiation / positive regulation of granulocyte colony-stimulating factor production / ventral spinal cord interneuron specification / spinal cord motor neuron cell fate specification / spinal cord association neuron differentiation / peripheral nervous system neuron development / cardiac cell fate determination / negative regulation of mesenchymal cell proliferation / thyroid-stimulating hormone-secreting cell differentiation / cardiac right ventricle morphogenesis / secondary heart field specification / regulation of secondary heart field cardioblast proliferation / atrial septum morphogenesis / positive regulation of type B pancreatic cell apoptotic process / neuron fate specification / bHLH transcription factor binding / pituitary gland development / spinal cord motor neuron differentiation / positive regulation of interleukin-1 alpha production / LIM domain binding / mesenchymal cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / neuron fate commitment / cardiac muscle cell myoblast differentiation / pharyngeal system development / outflow tract septum morphogenesis / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / pancreas development / motor neuron axon guidance / retinal ganglion cell axon guidance / positive regulation of granulocyte macrophage colony-stimulating factor production / innervation / neural crest cell migration / axon regeneration / endocardial cushion morphogenesis / cellular response to glucocorticoid stimulus / ventricular cardiac muscle tissue morphogenesis / negative regulation of neuron differentiation / positive regulation of calcium ion import / inner ear development / regulation of heart rate by cardiac conduction / outflow tract morphogenesis / positive regulation of vascular endothelial growth factor production / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / heart morphogenesis / core promoter sequence-specific DNA binding / positive regulation of interleukin-12 production / lung development / placenta development / positive regulation of interleukin-1 beta production / nuclear estrogen receptor binding / transcription coregulator binding / stem cell differentiation / positive regulation of cell differentiation / promoter-specific chromatin binding / negative regulation of canonical Wnt signaling pathway / positive regulation of insulin secretion / positive regulation of interleukin-6 production / negative regulation of inflammatory response / transcription coactivator binding / positive regulation of type II interferon production / neuron differentiation / positive regulation of angiogenesis / negative regulation of epithelial cell proliferation / positive regulation of tumor necrosis factor production / regulation of gene expression / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell population proliferation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / apoptotic process / chromatin binding / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm
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. ...: / : / : / : / : / 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 Lhx3 / Insulin gene enhancer protein ISL-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsBhati, M. / Lee, M. / Guss, J.M. / Matthews, J.M.
CitationJournal: Embo J. / Year: 2008
Title: Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes.
Authors: Bhati, M. / Lee, C. / Nancarrow, A.L. / Lee, M. / Craig, V.J. / Bach, I. / Guss, J.M. / Mackay, J.P. / Matthews, J.M.
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1
B: Fusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,73010
Polymers37,2062
Non-polymers5238
Water86548
1
A: Fusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1
hetero molecules

A: Fusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,73010
Polymers37,2062
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3060 Å2
ΔGint-26 kcal/mol
Surface area17790 Å2
MethodPISA
2
B: Fusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8655
Polymers18,6031
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.494, 62.218, 51.885
Angle α, β, γ (deg.)90.000, 91.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fusion of LIM/homeobox protein Lhx3, linker, Insulin gene enhancer protein ISL-1 / LIM homeobox protein 3 / Homeobox protein LIM-3 / Homeobox protein P-LIM / Islet-1


Mass: 18603.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fusion of Lhx3 residues 28-153 to Isl1 residues 262-291 via a glycine rich linker with sequence GGSGGHMGSGG
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) synthetic construct (others)
Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50481, UniProt: P61372
#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


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION OF LHX3 RESIDUES 28-153 TO ISL1 RESIDUES 262-291 VIA A GLYCINE RICH LINKER WITH SEQUENCE ...FUSION OF LHX3 RESIDUES 28-153 TO ISL1 RESIDUES 262-291 VIA A GLYCINE RICH LINKER WITH SEQUENCE GGSGGSGGSGG. RESIDUE NUMBERS 165-261 ARE SIMPLY SKIPPED.

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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: 2.59 Å3/Da / Density % sol: 52.53 % / Mosaicity: 1.036 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 1.0M tri-sodium citrate, 0.1M Tris, HCl pH 7.25, Vapour diffusion, Hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→59.76 Å / Num. obs: 23120 / % possible obs: 96.4 % / Rmerge(I) obs: 0.051 / Χ2: 1.055 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.120.38818551.048178.8
2.12-2.210.40521831.061191
2.21-2.310.28522971.053196.3
2.31-2.430.23623511.035199.2
2.43-2.580.18923991.068199.8
2.58-2.780.14123851.0591100
2.78-3.060.09224081.0791100
3.06-3.50.05223890.997199.9
3.5-4.410.02924011.088199.4
4.41-400.02424521.057199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
RefinementResolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.983 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1188 5.1 %RANDOM
Rwork0.211 ---
obs0.214 23109 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.103 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å2-1.34 Å2
2--4.26 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 8 48 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212417
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.9453257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8615298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22323.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92315406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1981519
X-RAY DIFFRACTIONr_chiral_restr0.1340.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021851
X-RAY DIFFRACTIONr_nbd_refined0.2330.2954
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.287
X-RAY DIFFRACTIONr_metal_ion_refined0.0730.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.29
X-RAY DIFFRACTIONr_mcbond_it1.0831.51544
X-RAY DIFFRACTIONr_mcangle_it1.72922407
X-RAY DIFFRACTIONr_scbond_it2.553982
X-RAY DIFFRACTIONr_scangle_it3.5984.5850
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 78 -
Rwork0.287 1275 -
all-1353 -
obs--78.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.34990.89561.96140.71260.9352.7448-0.08520.1058-0.18250.09070.09150.10280.342-0.0437-0.00630.0212-0.07490.0503-0.0450.0419-0.0621-7.221343.909210.2896
22.44211.7522.58281.2571.8532.7317-0.1974-0.26490.3081-0.2339-0.12480.1557-0.2835-0.06940.3222-0.0029-0.0292-0.04990.0704-0.03860.046816.267272.688712.9164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA32 - 1537 - 128
2X-RAY DIFFRACTION2BB26 - 1521 - 127

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