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- PDB-8ilw: Transcription factor LMX1a homeobox domain in complex with Pitx3 ... -

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Basic information

Entry
Database: PDB / ID: 8ilw
TitleTranscription factor LMX1a homeobox domain in complex with Pitx3 promoter
Components
  • DNA (5'-D(*CP*AP*AP*CP*AP*CP*TP*TP*AP*AP*TP*CP*CP*AP*AP*A)-3')
  • DNA (5'-D(*GP*TP*TP*TP*GP*GP*AP*TP*TP*AP*AP*GP*TP*GP*TP*T)-3')
  • LMX1A factor
KeywordsDNA BINDING PROTEIN/DNA / protein-dsDNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nucleus / metal ion binding
Similarity search - Function
Lmx1a, first LIM domain / 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. ...Lmx1a, first LIM domain / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / LMX1A factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.712 Å
AuthorsLv, M.Q. / Lin, L.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32293213, 32100958, 32090042 and 31870760 China
CitationJournal: Febs J. / Year: 2024
Title: Structural insights into the recognition of the A/T-rich motif in target gene promoters by the LMX1a homeobox domain
Authors: Lv, M.Q. / Lin, L.Q.
History
DepositionMar 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*CP*AP*AP*CP*AP*CP*TP*TP*AP*AP*TP*CP*CP*AP*AP*A)-3')
B: DNA (5'-D(*GP*TP*TP*TP*GP*GP*AP*TP*TP*AP*AP*GP*TP*GP*TP*T)-3')
C: LMX1A factor


Theoretical massNumber of molelcules
Total (without water)16,8273
Polymers16,8273
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-16 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.693, 51.486, 102.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*AP*AP*CP*AP*CP*TP*TP*AP*AP*TP*CP*CP*AP*AP*A)-3')


Mass: 4819.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*GP*TP*TP*TP*GP*GP*AP*TP*TP*AP*AP*GP*TP*GP*TP*T)-3')


Mass: 4974.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein LMX1A factor


Mass: 7033.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for homo sapiens is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A7K7QDL0.
Source: (gene. exp.) Homo sapiens (human) / Gene: Lmx1a, POEATR_R03507 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7K7QDL0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→34.59 Å / Num. obs: 7085 / % possible obs: 99.29 % / Redundancy: 9.7 % / CC1/2: 0.94 / Rmerge(I) obs: 0.118 / Net I/σ(I): 29.1
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2 / Num. unique obs: 536 / CC1/2: 0.905

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX3.3.22refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.712→34.588 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 36.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 536 7.57 %
Rwork0.2485 --
obs0.2512 7085 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.712→34.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms466 650 0 3 1119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121200
X-RAY DIFFRACTIONf_angle_d1.311754
X-RAY DIFFRACTIONf_dihedral_angle_d26.75609
X-RAY DIFFRACTIONf_chiral_restr0.063201
X-RAY DIFFRACTIONf_plane_restr0.007111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.712-2.98480.49841380.38441563X-RAY DIFFRACTION98
2.9848-3.41640.38211260.32081621X-RAY DIFFRACTION99
3.4164-4.3030.30751280.26641647X-RAY DIFFRACTION100
4.303-34.5880.21781440.20171718X-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)
10.36270.6007-1.12886.8145-1.40013.20950.49940.2950.3055-1.01090.40550.6098-0.45370.7083-0.66570.83650.039-0.00830.7231-0.09530.809413.3351.24161.5295
20.2307-0.2495-0.70483.3881-2.05833.82890.4271-0.15560.5864-0.01540.19870.2429-1.0299-0.3972-0.37790.99320.02870.03630.65480.08860.711610.3421.5445-1.6807
33.8148-1.1097-2.27083.3494-0.54711.7318-0.00570.46120.37610.1424-0.0380.1921-0.45620.36360.00020.3895-0.0533-0.03120.46980.02430.48778.1992-10.8625-3.6131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 16)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 16)
3X-RAY DIFFRACTION3(chain 'C' and resid 196 through 255)

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