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- PDB-2lfb: HOMEODOMAIN FROM RAT LIVER LFB1/HNF1 TRANSCRIPTION FACTOR, NMR, 2... -

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Basic information

Entry
Database: PDB / ID: 2lfb
TitleHOMEODOMAIN FROM RAT LIVER LFB1/HNF1 TRANSCRIPTION FACTOR, NMR, 20 STRUCTURES
ComponentsLFB1/HNF1 TRANSCRIPTION FACTOR
KeywordsDNA-BINDING / TRANSCRIPTION FACTOR / LFB1/HNF1 / HELIX-TURN-HELIX / DNA-BINDING DOMAIN
Function / homology
Function and homology information


paraxial mesoderm formation / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / cellular response to rapamycin / regulation of hormone secretion / reproductive structure development / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport ...paraxial mesoderm formation / apoptotic nuclear changes / regulation of NADP metabolic process / renal D-glucose absorption / cellular response to rapamycin / regulation of hormone secretion / reproductive structure development / bile acid biosynthetic process / cellular response to L-leucine / reverse cholesterol transport / pancreas development / negative regulation of miRNA processing / pronucleus / regulation of Wnt signaling pathway / embryonic limb morphogenesis / heme biosynthetic process / positive regulation of mitochondrial membrane potential / insulin secretion / bile acid and bile salt transport / D-glucose import / positive regulation of ATP biosynthetic process / blastocyst development / photoreceptor outer segment / positive regulation of transcription initiation by RNA polymerase II / bone resorption / response to glucose / fatty acid transport / cholesterol metabolic process / placenta development / transcription coregulator binding / cellular response to glucose stimulus / liver development / positive regulation of insulin secretion / transcription coactivator binding / fatty acid biosynthetic process / intracellular protein localization / glucose homeostasis / response to oxidative stress / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus ...Hepatocyte nuclear factor 1, alpha isoform C-terminal / Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus / Hepatocyte nuclear factor 1, beta isoform, C-terminal / Hepatocyte nuclear factor 1, N-terminal domain superfamily / Hepatocyte nuclear factor 1 / Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus / Hepatocyte nuclear factor 1, N-terminal / HNF-1, dimerization domain / HNF-1, POU-specific (POUs) atypical domain / Hepatocyte nuclear factor 1 (HNF-1), N terminus / POU-specific (POUs) atypical domain profile. / HNF-1 dimerization (HNF-p1) domain profile. / 'Homeobox' domain signature. / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hepatocyte nuclear factor 1-alpha
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodSOLUTION NMR / DISTANCE GEOMETRY WITH DIANA, ENERGY MINIMIZATION WITH OPAL
AuthorsSchott, O. / Billeter, M. / Leiting, B. / Wider, G. / Wuthrich, K.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The NMR solution structure of the non-classical homeodomain from the rat liver LFB1/HNF1 transcription factor.
Authors: Schott, O. / Billeter, M. / Leiting, B. / Wider, G. / Wuthrich, K.
#1: Journal: Embo J. / Year: 1993
Title: The Three-Dimensional NMR-Solution Structure of the Polypeptide Fragment 195-286 of the LFB1/HNF1 Transcription Factor from Rat Liver Comprises a Nonclassical Homeodomain
Authors: Leiting, B. / De Francesco, R. / Tomei, L. / Cortese, R. / Otting, G. / Wuthrich, K.
History
DepositionDec 12, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LFB1/HNF1 TRANSCRIPTION FACTOR


Theoretical massNumber of molelcules
Total (without water)11,8081
Polymers11,8081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50BEST TARGET FUNCTION
Representative

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Components

#1: Protein LFB1/HNF1 TRANSCRIPTION FACTOR


Mass: 11808.395 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 0 - 99, HOMEODOMAIN / Mutation: INS(MET0)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Organ: LIVER / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P15257

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-RESOLVED NOESY
12113C-RESOLVED NOESY
131J-MODULATED [15N
1411H]COSY

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Sample preparation

Sample conditionspH: 4.6 / Temperature: 295 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX 600 / Manufacturer: Bruker / Model: AMX 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
OPALLUGINBUHL,GUNTERT,BILLETER,WUTHRICHrefinement
BRUKER UXNMRUXNMRstructure solution
PROSAstructure solution
DIANAstructure solution
OPALstructure solution
RefinementMethod: DISTANCE GEOMETRY WITH DIANA, ENERGY MINIMIZATION WITH OPAL
Software ordinal: 1
NMR ensembleConformer selection criteria: BEST TARGET FUNCTION / Conformers calculated total number: 50 / Conformers submitted total number: 20

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