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- PDB-1pzl: Crystal structure of HNF4a LBD in complex with the ligand and the... -

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Basic information

Entry
Database: PDB / ID: 1pzl
TitleCrystal structure of HNF4a LBD in complex with the ligand and the coactivator SRC-1 peptide
Components
  • Hepatocyte nuclear factor 4-alpha
  • steroid receptor coactivator-1Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


regulation of growth hormone receptor signaling pathway / ornithine metabolic process / regulation of gastrulation / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / anatomical structure development / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose ...regulation of growth hormone receptor signaling pathway / ornithine metabolic process / regulation of gastrulation / sex differentiation / phospholipid homeostasis / signal transduction involved in regulation of gene expression / anatomical structure development / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / triglyceride homeostasis / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / lipid homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / regulation of lipid metabolic process / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / response to glucose / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / xenobiotic metabolic process / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / cholesterol homeostasis / fatty acid binding / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / lipid metabolic process / negative regulation of cell growth / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / rhythmic process / blood coagulation / Circadian Clock / sequence-specific double-stranded DNA binding / glucose homeostasis / response to estradiol / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / cell differentiation / transcription coactivator activity / transcription cis-regulatory region binding / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / 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 / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
: / : / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...: / : / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Nuclear receptor coactivator, interlocking / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MYRISTIC ACID / : / Hepatocyte nuclear factor 4-alpha / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDuda, K. / Chi, Y.-I. / Dhe-paganon, S. / Shoelson, S.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Basis for HNF-4alpha Activation by Ligand and Coactivator Binding
Authors: Duda, K. / Chi, Y.-I. / Shoelson, S.
History
DepositionJul 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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: Hepatocyte nuclear factor 4-alpha
B: steroid receptor coactivator-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5783
Polymers28,3502
Non-polymers2281
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-4 kcal/mol
Surface area12130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.491, 81.491, 104.709
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hepatocyte nuclear factor 4-alpha / HNF-4-alpha / Transcription factor HNF-4 / Transcription factor 14


Mass: 26731.016 Da / Num. of mol.: 1 / Fragment: HNF4A-LDB / Mutation: D137L, S138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4A / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P41235
#2: Protein/peptide steroid receptor coactivator-1 / Nuclear receptor coactivator 1 / SRC-1


Mass: 1618.878 Da / Num. of mol.: 1 / Fragment: NRbox2 peptide of SRC-1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: GenBank: 1906028, UniProt: Q15788*PLUS
#3: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.06 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium, Potassium Tartrate, Hepes, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97904 Å
DetectorType: BRANDEIS - B2 / Detector: CCD / Date: Nov 11, 2002
RadiationMonochromator: Si-double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.1→29.9 Å / Num. all: 20187 / Num. obs: 20180 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 29.7 Å2 / Rsym value: 0.047 / Net I/σ(I): 32.7
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 3.59 / Num. unique all: 798 / Rsym value: 0.225 / % possible all: 76.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 966 -5% data
Rwork0.226 ---
all0.23 20155 --
obs0.229 19984 94.2 %-
Displacement parametersBiso mean: 42.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.568 Å20 Å20 Å2
2--3.568 Å20 Å2
3----7.136 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 16 138 2074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.078
X-RAY DIFFRACTIONc_improper_angle_d0.746
X-RAY DIFFRACTIONc_dihedral_angle_d18.916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.1-2.140.3249300.2882X-RAY DIFFRACTION7596
2.38-2.450.2425420.2486X-RAY DIFFRACTION10136
2.69-2.80.254630.2372X-RAY DIFFRACTION10206
3.08-3.270.2708420.2451X-RAY DIFFRACTION10556
3.88-4.430.2231520.1929X-RAY DIFFRACTION10736
5.57-200.2584760.2112X-RAY DIFFRACTION11566

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