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- PDB-8ike: Transcription factors LMX1a mutant-R199A homeobox domain complex ... -

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Basic information

Entry
Database: PDB / ID: 8ike
TitleTranscription factors LMX1a mutant-R199A homeobox domain complex with Wnt1 promoter
Components
  • DNA (5'-D(*CP*CP*AP*TP*AP*TP*TP*TP*AP*AP*TP*CP*TP*TP*C)-3')
  • DNA (5'-D(*GP*GP*AP*AP*GP*AP*TP*TP*AP*AP*AP*TP*AP*TP*G)-3')
  • LMX1A factor
KeywordsDNA BINDING PROTEIN/DNA / protein-dsDNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / DNA binding / 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 ...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: 2.6 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
DepositionFeb 28, 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

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Assembly

Deposited unit
A: DNA (5'-D(*CP*CP*AP*TP*AP*TP*TP*TP*AP*AP*TP*CP*TP*TP*C)-3')
B: DNA (5'-D(*GP*GP*AP*AP*GP*AP*TP*TP*AP*AP*AP*TP*AP*TP*G)-3')
C: LMX1A factor


Theoretical massNumber of molelcules
Total (without water)16,1503
Polymers16,1503
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-16 kcal/mol
Surface area8630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.637, 47.303, 95.912
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*CP*AP*TP*AP*TP*TP*TP*AP*AP*TP*CP*TP*TP*C)-3')


Mass: 4493.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*GP*GP*AP*AP*GP*AP*TP*TP*AP*AP*AP*TP*AP*TP*G)-3')


Mass: 4681.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein LMX1A factor


Mass: 6975.224 Da / Num. of mol.: 1 / Mutation: R199A
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.: 23 / 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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 4000, 0.2 mM MES monohydrate (PH 5.9)

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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: 2.6→27.3 Å / Num. obs: 6915 / % possible obs: 99.6 % / Redundancy: 12.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 12 % / Rmerge(I) obs: 0.6026 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 664 / CC1/2: 0.998 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX3.3.22refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→27.3 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2624 665 9.63 %
Rwork0.228 --
obs0.2313 6902 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms466 609 0 23 1098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041154
X-RAY DIFFRACTIONf_angle_d0.6461684
X-RAY DIFFRACTIONf_dihedral_angle_d24.768588
X-RAY DIFFRACTIONf_chiral_restr0.029193
X-RAY DIFFRACTIONf_plane_restr0.002110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6003-2.80090.36131160.33641223X-RAY DIFFRACTION100
2.8009-3.08240.39671330.32181223X-RAY DIFFRACTION100
3.0824-3.52770.31331390.27371217X-RAY DIFFRACTION99
3.5277-4.44140.24191170.21211266X-RAY DIFFRACTION100
4.4414-27.30.20271600.1751308X-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)
15.71480.8479-1.01993.64251.33897.48240.26550.32280.3988-0.30770.20610.0761-1.2804-0.2262-0.51960.64250.11060.00180.38870.02390.5238-13.45732.9272-0.8916
24.2824-0.8018-2.17185.02470.18966.26450.2518-0.20320.46110.19960.1721-0.0478-1.06330.1875-0.47990.5073-0.0142-0.01370.434-0.06550.4676-11.01691.81512.778
35.2440.12110.10114.1474-0.16664.9202-0.0272-0.4434-0.21740.25820.0640.1533-0.0585-0.2298-0.09230.3378-0.00880.01430.3250.02350.3779-8.477-10.5913.9885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 15)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 15)
3X-RAY DIFFRACTION3(chain 'C' and resid 197 through 256)

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