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- PDB-8ik5: Transcription factor LMX1a homeobox domain in complex with Wnt1 p... -

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Basic information

Entry
Database: PDB / ID: 8ik5
TitleTranscription factor LMX1a homeobox domain in 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 / metal ion binding / nucleus
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: 1.989 Å
AuthorsLv, M.Q. / Lin, L.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32293213, 32100958, 32090042, 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3415
Polymers17,1573
Non-polymers1842
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-19 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.290, 46.419, 96.098
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: 7981.499 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) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7K7QDL0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 27% PEG MME 2000, 0.1 mM sodium cacodylate (pH 6.5)

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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: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.989→27.08 Å / Num. obs: 14659 / % possible obs: 99.08 % / Redundancy: 10.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.065 / Net I/σ(I): 33.7
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 707 / CC1/2: 0.909

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX3.3.22refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.989→27.077 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 707 4.82 %
Rwork0.2066 --
obs0.2081 14659 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.989→27.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms532 609 12 71 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081233
X-RAY DIFFRACTIONf_angle_d0.9521785
X-RAY DIFFRACTIONf_dihedral_angle_d24.415637
X-RAY DIFFRACTIONf_chiral_restr0.043200
X-RAY DIFFRACTIONf_plane_restr0.005122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.989-2.14250.32241400.26162664X-RAY DIFFRACTION97
2.1425-2.35790.30051330.23762771X-RAY DIFFRACTION100
2.3579-2.69890.30211390.24712782X-RAY DIFFRACTION100
2.6989-3.39930.2511440.2322794X-RAY DIFFRACTION99
3.3993-27.0770.19631510.17612941X-RAY DIFFRACTION99
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)
14.6054-0.79310.73935.9212-0.16587.88950.241-0.26280.06540.1530.2350.7124-0.24-1.5128-0.36530.34890.04920.00230.55780.0330.37428.48961.789326.4771
25.1667-0.1793-0.35165.4248-1.13346.78790.25260.2194-0.0934-0.29670.15250.5261-0.1496-1.5371-0.32260.3560.0313-0.02820.5283-0.00380.31339.2975-0.60322.7996
33.9082-0.3470.4087.71340.19123.8750.07740.4636-0.0833-0.4048-0.2153-0.0034-0.0502-0.2580.0860.25430.0310.03120.3288-0.02530.194119.8454-1.16319.8356
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 190 through 256)

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