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Basic information

Entry
Database: PDB / ID: 3mmk
TitleThe structural basis for partial redundancy in a class of transcription factors, the lim-homeodomain proteins, in neural cell type specification
ComponentsFusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
KeywordsMETAL BINDING PROTEIN / Protein-protein complex / LIM domain / Zn finger / DNA-binding / Homeobox / Metal-binding / Nucleus / Transcription / Transcriptional regulation
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 / SYNCHROTRON / SAD / Resolution: 2.157 Å
AuthorsGadd, M.S. / Langley, D.B. / Guss, J.M. / Matthews, J.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The structural basis for partial redundancy in a class of transcription factors, the lim-homeodomain proteins, in neural cell type specification.
Authors: Gadd, M.S. / Bhati, M. / Jeffries, C.M. / Langley, D.B. / Trewhella, J. / Guss, J.M. / Matthews, J.M.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references / Structure summary
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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 Lhx4, linker, Insulin gene enhancer protein ISL-2
B: Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,96414
Polymers37,2992
Non-polymers66512
Water55831
1
A: Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0178
Polymers18,6491
Non-polymers3687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fusion of LIM/homeobox protein Lhx4, linker, Insulin gene enhancer protein ISL-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9466
Polymers18,6491
Non-polymers2975
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.823, 88.734, 49.851
Angle α, β, γ (deg.)90.00, 111.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18649.264 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 24-149 AND 272-301
Source method: isolated from a genetically manipulated source
Details: Fusion of Lhx4 residues 24-149 to Isl2 residues 272-301 via a glycine rich linker with sequence GGSGGHMGSGG
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsh-4, Gsh4, Isl2, Lhx4 / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / 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: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFUSION OF LHX4 RESIDUES 24-149 TO ISL2 RESIDUES 272-301 VIA A GLYCINE RICH LINKER WITH SEQUENCE GGSGGHMGSGG

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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: 2.58 Å3/Da / Density % sol: 52.27 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M magnesium sulphate, 0.1M MES, 3% (w/v) sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.2819 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.157→50 Å / Num. all: 20403 / Num. obs: 20403 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 52.61 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.269
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2.458 / Rsym value: 0.473 / % possible all: 78.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.157→23.135 Å / SU ML: 0.41 / Isotropic thermal model: Isotropic / σ(F): 1.9 / Phase error: 32.04 / Stereochemistry target values: ML / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 2022 5.16 %Random
Rwork0.2348 ---
obs0.2366 20403 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.962 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.8478 Å20 Å2-6.3283 Å2
2---11.0396 Å20 Å2
3---5.1918 Å2
Refinement stepCycle: LAST / Resolution: 2.157→23.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 12 31 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032239
X-RAY DIFFRACTIONf_angle_d0.6553044
X-RAY DIFFRACTIONf_dihedral_angle_d13.402730
X-RAY DIFFRACTIONf_chiral_restr0.048344
X-RAY DIFFRACTIONf_plane_restr0.002400
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1572-2.21110.3137920.2938231585
2.2111-2.27080.3851280.3042259995
2.2708-2.33760.31091440.2976266398
2.3376-2.41290.32231750.26922644100
2.4129-2.49910.28231470.274272699
2.4991-2.5990.31991390.24692754100
2.599-2.71710.30321320.26672668100
2.7171-2.86010.26891420.27732738100
2.8601-3.03890.29741760.25642671100
3.0389-3.2730.32051300.2682719100
3.273-3.60130.32381530.2093272599
3.6013-4.11980.19981440.1937266899
4.1198-5.18090.19411380.1749269198
5.1809-23.13620.21911820.2208258897
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)
10.25240.4456-0.420.65820.2291-0.0790.12130.11390.3795-0.17990.14330.00580.33510.2017-0.00010.50540.0325-0.15730.4533-0.06430.542836.311681.250541.2282
20.06890.4065-0.3107-0.00440.02540.1697-0.3959-0.09650.1814-0.07750.1777-0.09460.61730.2711-0.00020.7254-0.0483-0.19080.4858-0.04310.523731.268172.476529.4301
30.6168-0.4263-1.16711.83831.61572.08950.0327-0.0519-0.167-0.35030.07910.1377-0.59410.19860.00010.4-0.0668-0.06110.40520.00890.344715.46253.731334.4046
40.1090.7194-0.78810.1282-0.00660.14370.1032-0.24070.85740.34110.49480.50210.6481-0.4869-0.00620.4832-0.0159-0.00910.6215-0.19670.732226.517880.318342.6891
50.09740.81230.00830.67750.9743-0.30650.21480.1038-0.04910.0874-0.01980.0915-0.34350.27540.00010.5237-0.00150.12490.3821-0.03720.532510.961923.373455.5941
60.97291.11580.36250.49280.55471.4096-0.01740.03540.17410.1650.02980.11650.50080.01590.00040.36360.04270.05210.3505-0.02050.3262-7.620447.680958.7592
7-0.3775-0.48620.31580.2737-0.62390.32950.14880.38580.1933-0.40650.141-0.0244-0.3105-0.58340.00010.61340.1189-0.00530.6437-0.08660.53574.10119.212647.1196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 26:61)
2X-RAY DIFFRACTION2(chain A and resid 62:86)
3X-RAY DIFFRACTION3(chain A and resid 87:286)
4X-RAY DIFFRACTION4(chain A and resid 287:299)
5X-RAY DIFFRACTION5(chain B and resid 26:85)
6X-RAY DIFFRACTION6(chain B and resid 86:285)
7X-RAY DIFFRACTION7(chain B and resid 286:301)

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