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- PDB-3cbb: Crystal Structure of Hepatocyte Nuclear Factor 4alpha in complex ... -

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Basic information

Entry
Database: PDB / ID: 3cbb
TitleCrystal Structure of Hepatocyte Nuclear Factor 4alpha in complex with DNA: Diabetes Gene Product
Components
  • (Hepatocyte Nuclear Factor 4-alpha promoter element DNA) x 2
  • Hepatocyte Nuclear Factor 4-alpha, DNA binding domain
KeywordsTRANSCRIPTION/DNA / zinc finger / protein-DNA complex / diabetes / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of growth hormone receptor signaling pathway / ornithine metabolic process / regulation of gastrulation / Nephron development / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / triglyceride homeostasis / lipid homeostasis / Regulation of gene expression in beta cells ...regulation of growth hormone receptor signaling pathway / ornithine metabolic process / regulation of gastrulation / Nephron development / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / triglyceride homeostasis / lipid homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / regulation of lipid metabolic process / response to glucose / xenobiotic metabolic process / cholesterol homeostasis / fatty acid binding / regulation of circadian rhythm / lipid metabolic process / negative regulation of cell growth / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / blood coagulation / rhythmic process / glucose homeostasis / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...: / : / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Hepatocyte nuclear factor 4-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLu, P. / Rha, G.B. / Melikishvili, M. / Adkins, B.C. / Fried, M.G. / Chi, Y.I.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4alpha. Diabetes gene product.
Authors: Lu, P. / Rha, G.B. / Melikishvili, M. / Wu, G. / Adkins, B.C. / Fried, M.G. / Chi, Y.I.
#1: Journal: To be Published
Title: Crystallization of Hepatocyte Nuclear Factor 4alpha (HNF4alpha) in complex with the HNF1alpha Promoter Element
Authors: Lu, P. / Liu, J. / Melikishvili, M. / Fried, M.G. / Chi, Y.-I.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Hepatocyte Nuclear Factor 4-alpha promoter element DNA
D: Hepatocyte Nuclear Factor 4-alpha promoter element DNA
A: Hepatocyte Nuclear Factor 4-alpha, DNA binding domain
B: Hepatocyte Nuclear Factor 4-alpha, DNA binding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2608
Polymers30,9994
Non-polymers2624
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-29 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.628, 35.425, 70.985
Angle α, β, γ (deg.)90.000, 119.360, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain Hepatocyte Nuclear Factor 4-alpha promoter element DNA


Mass: 6407.160 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain Hepatocyte Nuclear Factor 4-alpha promoter element DNA


Mass: 6478.195 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Hepatocyte Nuclear Factor 4-alpha, DNA binding domain / HNF-4-alpha / Transcription factor HNF-4 / Nuclear receptor subfamily 2 group A member 1 / ...HNF-4-alpha / Transcription factor HNF-4 / Nuclear receptor subfamily 2 group A member 1 / Transcription factor 14


Mass: 9056.581 Da / Num. of mol.: 2 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4A, HNF4, NR2A1, TCF14 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41235
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 26% PEG 4000, 80mM Magnesium acetate, 50mM Sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Magnesium acetate11
3Sodium citrate11
4PEG 400012
5Magnesium acetate12
6Sodium citrate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.92017 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2006
RadiationMonochromator: Rosenbaum-Rock Monochromator High-Resolution Double-Crystal SI (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92017 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 17094 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.064 / Χ2: 1.299 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.304 / Num. unique all: 1294 / Χ2: 0.886 / % possible all: 72.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.514 / Cor.coef. Fo:Fc: 0.385
Highest resolutionLowest resolution
Rotation3 Å30.33 Å
Translation3 Å30.33 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / FOM work R set: 0.839 / σ(F): 2
RfactorNum. reflection
Rfree0.252 811
Rwork0.213 -
obs-16841
Displacement parametersBiso mean: 28.169 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1230 855 4 157 2246
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.031
X-RAY DIFFRACTIONx_dihedral_angle_d19.506
X-RAY DIFFRACTIONx_improper_angle_d1.15

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