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- PDB-2h8r: Hepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product -

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Basic information

Entry
Database: PDB / ID: 2h8r
TitleHepatocyte Nuclear Factor 1b bound to DNA: MODY5 Gene Product
Components
  • 5'-D(*CP*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*TP*CP*AP*CP*CP*AP*G)-3'
  • 5'-D(*GP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*A)-3'
  • Hepatocyte nuclear factor 1-beta
KeywordsTRANSCRIPTION ACTIVATOR/DNA / trasncription factor / POU / homeo / protein-DNA / human disease / TRANSCRIPTION ACTIVATOR-DNA COMPLEX
Function / homology
Function and homology information


regulation of pronephros size / pronephric nephron tubule development / ureteric bud elongation / hepatoblast differentiation / negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis / mesonephric duct formation / mesenchymal cell apoptotic process involved in metanephros development / regulation of branch elongation involved in ureteric bud branching / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development ...regulation of pronephros size / pronephric nephron tubule development / ureteric bud elongation / hepatoblast differentiation / negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis / mesonephric duct formation / mesenchymal cell apoptotic process involved in metanephros development / regulation of branch elongation involved in ureteric bud branching / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development / Regulation of gene expression in early pancreatic precursor cells / inner cell mass cell differentiation / endodermal cell fate specification / genitalia development / embryonic digestive tract morphogenesis / hindbrain development / endocrine pancreas development / pancreas development / regulation of Wnt signaling pathway / insulin secretion / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / anterior/posterior pattern specification / branching morphogenesis of an epithelial tube / positive regulation of transcription initiation by RNA polymerase II / response to glucose / Notch signaling pathway / epithelial cell proliferation / kidney development / transcription coregulator binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
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. ...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 / lambda repressor-like DNA-binding domains / Homeobox domain / 434 Repressor (Amino-terminal 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
DNA / DNA (> 10) / Hepatocyte nuclear factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLu, P. / Rha, G.B. / Chi, Y.I.
Citation
Journal: Biochemistry / Year: 2007
Title: Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta.
Authors: Lu, P. / Rha, G.B. / Chi, Y.I.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization of hepatocyte nuclear factor 1beta in complex with DNA.
Authors: Lu, P. / Li, Y. / Gorman, A. / Chi, Y.I.
History
DepositionJun 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*CP*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*TP*CP*AP*CP*CP*AP*G)-3'
F: 5'-D(*GP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*A)-3'
A: Hepatocyte nuclear factor 1-beta
B: Hepatocyte nuclear factor 1-beta


Theoretical massNumber of molelcules
Total (without water)63,6894
Polymers63,6894
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.689, 174.689, 72.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsDimer when binding to DNA

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Components

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


Mass: 6107.977 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*A)-3'


Mass: 6157.016 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Hepatocyte nuclear factor 1-beta / HNF-1beta / HNF-1B / Variant hepatic nuclear factor 1 / VHNF1 / Homeoprotein LFB3 / Transcription ...HNF-1beta / HNF-1B / Variant hepatic nuclear factor 1 / VHNF1 / Homeoprotein LFB3 / Transcription factor 2 / TCF-2


Mass: 25711.850 Da / Num. of mol.: 2 / Fragment: DNA Binding Domain (residues 91-310)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET41a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35680
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6%(v/v) PEG300, 5%(v/v) PEG8000, 8%(v/v) glycerol, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG30011
2PEG800011
3glycerol11
4Tris11
5H2O11
6PEG30012
7PEG800012
8Tris12
9H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97923 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2005
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 3.2→27.9 Å / Num. all: 12635 / Num. obs: 12582 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 57.24 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.083 / Net I/σ(I): 28.8
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.35 / Rsym value: 0.273 / % possible all: 63.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-2000data reduction
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IC8

1ic8


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.829 / SU B: 21.564 / SU ML: 0.374 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.538 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 637 5 %RANDOM
Rwork0.22292 ---
obs0.22614 11992 93.26 %-
all-12582 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.209 Å2
Baniso -1Baniso -2Baniso -3
1-5.43 Å22.72 Å20 Å2
2--5.43 Å20 Å2
3----8.15 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 814 0 7 3737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0790.0213866
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg5.452.2065362
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.0425348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2580.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.020.022697
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3740.22269
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2940.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.212
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.470.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5421.51756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.67822814
X-RAY DIFFRACTIONr_scbond_it5.74532110
X-RAY DIFFRACTIONr_scangle_it8.6744.52548
X-RAY DIFFRACTIONr_rigid_bond_restr3.68623866
X-RAY DIFFRACTIONr_sphericity_free20.23927
X-RAY DIFFRACTIONr_sphericity_bonded5.17423717
LS refinement shellResolution: 3.201→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 24 -
Rwork0.23 528 -
obs--53.3 %

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