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- PDB-5hod: Structure of LHX4 transcription factor complexed with DNA -

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Basic information

Entry
Database: PDB / ID: 5hod
TitleStructure of LHX4 transcription factor complexed with DNA
Components
  • DNA (5'-D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP*TP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*AP*AP*TP*TP*AP*CP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*T)-3')
  • LIM/homeobox protein Lhx4
KeywordsTRANSCRIPTION / Transcription factor / Complex with DNA / Dimer
Function / homology
Function and homology information


medial motor column neuron differentiation / methyl-CpG binding / motor neuron axon guidance / placenta development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / neuron differentiation / Regulation of expression of SLITs and ROBOs / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific ...medial motor column neuron differentiation / methyl-CpG binding / motor neuron axon guidance / placenta development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / neuron differentiation / Regulation of expression of SLITs and ROBOs / 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 / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / metal ion binding / nucleus
Similarity search - Function
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 ...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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / LIM/homeobox protein Lhx4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.682 Å
AuthorsMorgunova, E. / Yin, Y. / Popov, A. / Taipale, J.
CitationJournal: Science / Year: 2017
Title: Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / ...Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / Domcke, S. / Yan, J. / Schubeler, D. / Vinson, C. / Taipale, J.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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
B: DNA (5'-D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP*TP*AP*G)-3')
C: DNA (5'-D(P*CP*TP*AP*AP*TP*TP*AP*CP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*T)-3')
D: LIM/homeobox protein Lhx4


Theoretical massNumber of molelcules
Total (without water)26,5944
Polymers26,5944
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-23 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.768, 68.442, 200.464
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

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Components

#1: Protein LIM/homeobox protein Lhx4 / LIM homeobox protein 4


Mass: 7164.329 Da / Num. of mol.: 2 / Fragment: UNP residues 156-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LHX4 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q969G2
#2: DNA chain DNA (5'-D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP*TP*AP*G)-3')


Mass: 6157.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*CP*TP*AP*AP*TP*TP*AP*CP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*T)-3')


Mass: 6107.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000,Tris buffer, magnesium chloride, MPD / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.682→50 Å / Num. obs: 8245 / % possible obs: 98.79 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 2.682→2.77 Å / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 1.55 / % possible all: 91.77

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BW5

1bw5


Resolution: 2.682→50.116 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0.52 / Phase error: 35.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.261 772 5.15 %Random
Rwork0.2332 ---
obs0.2347 8147 98.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.682→50.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 820 0 27 1833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051918
X-RAY DIFFRACTIONf_angle_d0.8842749
X-RAY DIFFRACTIONf_dihedral_angle_d26.423805
X-RAY DIFFRACTIONf_chiral_restr0.246306
X-RAY DIFFRACTIONf_plane_restr0.003211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6816-2.84960.42191150.35042292X-RAY DIFFRACTION95
2.8496-3.06960.39231390.33922372X-RAY DIFFRACTION99
3.0696-3.37840.36541180.29512397X-RAY DIFFRACTION100
3.3784-3.86710.3242910.25542420X-RAY DIFFRACTION99
3.8671-4.87150.26581600.22232362X-RAY DIFFRACTION100
4.8715-50.12470.19831490.18622385X-RAY DIFFRACTION100
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)
10.85370.30730.78822.3619-0.10910.9530.18090.42470.20580.3392-0.38590.3218-0.040.03620.58030.3367-0.0290.08260.5010.0450.641946.522415.81246.2295
21.0462-0.9598-0.60160.5812-0.46650.990.4542-1.1237-1.0640.69090.0149-1.06860.2471-0.46430.02551.1759-0.2922-0.55851.09970.23810.947958.73745.612327.604
31.11560.1034-0.88720.59920.34820.4058-0.3189-1.299-0.25690.4942-0.0792-0.2652-0.45990.6852-0.34731.0798-0.1711-0.42771.62180.18750.8658.58335.37727.0994
40.14070.069-0.03830.0717-0.1670.0939-0.26950.44890.2912-1.1070.14940.3017-0.5276-0.577-0.00011.769-0.09510.34172.2354-0.50312.265170.247618.594528.9851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 88 through 144 )
2X-RAY DIFFRACTION2chain B and (resid 1 through 20 )
3X-RAY DIFFRACTION3chain C and (resid 21 through 40 )
4X-RAY DIFFRACTION4chain D and (resid 87 through 144 )

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