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- PDB-2lef: LEF1 HMG DOMAIN (FROM MOUSE), COMPLEXED WITH DNA (15BP), NMR, 12 ... -

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Basic information

Entry
Database: PDB / ID: 2lef
TitleLEF1 HMG DOMAIN (FROM MOUSE), COMPLEXED WITH DNA (15BP), NMR, 12 STRUCTURES
Components
  • DNA (5'-D(*CP*AP*CP*CP*CP*TP*TP*TP*GP*AP*AP*GP*CP*TP*C)-3')
  • DNA (5'-D(*GP*AP*GP*CP*TP*TP*CP*AP*AP*AP*GP*GP*GP*TP*G)-3')
  • PROTEIN (LYMPHOID ENHANCER-BINDING FACTOR)
KeywordsGENE REGULATION/DNA / LEF1 / HMG / TCR-A / TRANSCRIPTION FACTOR / DNA BINDING / DNA BENDING / COMPLEX (HMG DOMAIN-DNA) / GENE REGULATION-DNA COMPLEX
Function / homology
Function and homology information


Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / RUNX3 regulates WNT signaling / negative regulation of interleukin-4 production / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of granulocyte differentiation ...Repression of WNT target genes / forebrain neuroblast division / trachea gland development / paraxial mesoderm formation / chorio-allantoic fusion / anatomical structure regression / RUNX3 regulates WNT signaling / negative regulation of interleukin-4 production / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / positive regulation of granulocyte differentiation / T cell receptor V(D)J recombination / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / neutrophil differentiation / negative regulation of apoptotic process in bone marrow cell / negative regulation of striated muscle tissue development / T-helper 1 cell differentiation / Formation of the beta-catenin:TCF transactivating complex / armadillo repeat domain binding / Deactivation of the beta-catenin transactivating complex / apoptotic process involved in blood vessel morphogenesis / formation of radial glial scaffolds / positive regulation of cell proliferation in bone marrow / Ca2+ pathway / apoptotic process involved in morphogenesis / odontoblast differentiation / secondary palate development / cell development / beta-catenin-TCF complex / gamma-catenin binding / positive regulation of gamma-delta T cell differentiation / positive regulation of odontoblast differentiation / mammary gland development / forebrain radial glial cell differentiation / positive regulation of chondrocyte proliferation / dentate gyrus development / vasculature development / C2H2 zinc finger domain binding / regulation of Wnt signaling pathway / positive regulation by host of viral transcription / transcription regulator inhibitor activity / embryonic limb morphogenesis / face morphogenesis / sprouting angiogenesis / tongue development / DNA binding, bending / alpha-beta T cell differentiation / epithelial cell apoptotic process / branching involved in blood vessel morphogenesis / odontogenesis of dentin-containing tooth / B cell proliferation / regulation of cell-cell adhesion / positive regulation of Wnt signaling pathway / regulation of neurogenesis / epithelial to mesenchymal transition / somitogenesis / canonical Wnt signaling pathway / cellular response to interleukin-4 / BMP signaling pathway / cis-regulatory region sequence-specific DNA binding / positive regulation of epithelial to mesenchymal transition / protein localization to chromatin / cell chemotaxis / transcription corepressor binding / hippocampus development / nuclear estrogen receptor binding / positive regulation of cell differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / beta-catenin binding / histone deacetylase binding / osteoblast differentiation / RNA polymerase II transcription regulator complex / sensory perception of taste / histone binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / High mobility group box domain / DNA Binding (I), subunit A / Catenin binding domain superfamily / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain ...CTNNB1 binding, N-teminal / N-terminal CTNNB1 binding / Transcription factor TCF/LEF / High mobility group box domain / DNA Binding (I), subunit A / Catenin binding domain superfamily / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Lymphoid enhancer-binding factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DG IN TORSION SPACE (DIANA), DYNAMICAL SIMULATED ANNEALING
AuthorsLi, X. / Love, J.J. / Case, D.A. / Wright, P.E.
CitationJournal: Nature / Year: 1995
Title: Structural basis for DNA bending by the architectural transcription factor LEF-1.
Authors: Love, J.J. / Li, X. / Case, D.A. / Giese, K. / Grosschedl, R. / Wright, P.E.
History
DepositionOct 13, 1998Deposition site: BNL / Processing site: RCSB
SupersessionOct 21, 1998ID: 1LEF
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*CP*AP*CP*CP*CP*TP*TP*TP*GP*AP*AP*GP*CP*TP*C)-3')
C: DNA (5'-D(*GP*AP*GP*CP*TP*TP*CP*AP*AP*AP*GP*GP*GP*TP*G)-3')
A: PROTEIN (LYMPHOID ENHANCER-BINDING FACTOR)


Theoretical massNumber of molelcules
Total (without water)19,5823
Polymers19,5823
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 28CONSTRAINTS VIOLATION, AMBER ENERGIES
RepresentativeModel #3

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Components

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


Mass: 4504.936 Da / Num. of mol.: 1 / Fragment: LEF-1 BINDING SITE / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*AP*GP*CP*TP*TP*CP*AP*AP*AP*GP*GP*GP*TP*G)-3')


Mass: 4674.046 Da / Num. of mol.: 1 / Fragment: LEF-1 BINDING SITE / Source method: obtained synthetically
#3: Protein PROTEIN (LYMPHOID ENHANCER-BINDING FACTOR) / LEF-1 HMG


Mass: 10403.220 Da / Num. of mol.: 1 / Fragment: HMG / Mutation: CHAIN A, C25S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BL21 (DE3) / Cell: PRE-B AND T LYMPHOCYTE / Gene: LEF1 / Plasmid: PET-21A / Species (production host): Escherichia coli / Gene (production host): LEF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P27782

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CT-HNCA
121CBCA(CO)NH
131HN(CA)CB
141C(CO)NH-TOCSY
151(H)CCH-COSY
161(H)CCH-TOCSY
171(15N)3D NOESY-HSQC
181(13C)3D NOESY-HSQC
191(13C/13C)4D HMQC-NOESY-HMQC
11012D 13C/15N DOUBLE HALF-FILTERED NOESY
11113D 13C-SELECTED(W1
1121W2) 12C-FILTERED (W3) NOESY
11312D 1H NOESY
1141AROMATIC 13C CT-HSQC
1151HNCA-J
1161HNHA
1171HNHB
1181HACAHB-COSY
1191HMBC
12013D LRCC
NMR detailsText: PRESSURE: 1 ATM SOLVENT SYSTEM: 90%H2O/10%D2O,

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Sample preparation

Sample conditionsIonic strength: 10 mM KCL / pH: 6.7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker AMX600BrukerAMX6006002
Bruker DMX750BrukerDMX7507503

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Processing

NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
Felixstructure solution
DIANAstructure solution
Amberstructure solution
RefinementMethod: DG IN TORSION SPACE (DIANA), DYNAMICAL SIMULATED ANNEALING
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: CONSTRAINTS VIOLATION, AMBER ENERGIES
Conformers calculated total number: 28 / Conformers submitted total number: 12

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