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- PDB-1m7w: HNF4a ligand binding domain with bound fatty acid -

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Basic information

Entry
Database: PDB / ID: 1m7w
TitleHNF4a ligand binding domain with bound fatty acid
ComponentsHepatocyte nuclear factor 4-alpha
KeywordsTRANSCRIPTION FACTOR
Function / homology
Function and homology information


establishment of tissue polarity / negative regulation of activation of Janus kinase activity / stearic acid binding / ornithine metabolic process / DNA-binding transcription factor binding => GO:0140297 / long-chain fatty acyl-CoA binding / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / regulation of gastrulation / : / regulation of microvillus assembly ...establishment of tissue polarity / negative regulation of activation of Janus kinase activity / stearic acid binding / ornithine metabolic process / DNA-binding transcription factor binding => GO:0140297 / long-chain fatty acyl-CoA binding / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / regulation of gastrulation / : / regulation of microvillus assembly / acyl-CoA metabolic process / : / fatty-acyl-CoA binding / response to xenobiotic stimulus => GO:0009410 / sex differentiation / Nuclear Receptor transcription pathway / negative regulation of tyrosine phosphorylation of STAT protein / type B pancreatic cell development / phospholipid homeostasis / positive regulation of fatty acid biosynthetic process / signal transduction involved in regulation of gene expression / cell-cell junction organization / triglyceride homeostasis / hepatocyte differentiation / SMAD protein signal transduction / anatomical structure development / arachidonic acid binding / negative regulation of protein import into nucleus / response to dexamethasone / lipid homeostasis / regulation of insulin secretion / transcription factor binding / regulation of lipid metabolic process / negative regulation of mitotic cell cycle / cis-regulatory region sequence-specific DNA binding / response to glucose / positive regulation of gluconeogenesis / response to cAMP / xenobiotic metabolic process / response to nutrient levels / cholesterol homeostasis / negative regulation of cell migration / fatty acid binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lipid metabolic process / negative regulation of DNA-binding transcription factor activity / regulation of circadian rhythm / negative regulation of cell growth / rhythmic process / blood coagulation / glucose homeostasis / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / response to lipopolysaccharide / 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 / protein-containing complex binding / regulation of DNA-templated transcription / 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 / nucleus / cytoplasm
Similarity search - Function
Hepatocyte nuclear factor 4-alpha / 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 ...Hepatocyte nuclear factor 4-alpha / 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
LAURIC ACID / Hepatocyte nuclear factor 4-alpha
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsDhe-Paganon, S. / Duda, K. / Iwamoto, M. / Chi, Y.I. / Shoelson, S.E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the HNF4 alpha ligand binding domain in complex with endogenous fatty acid ligand
Authors: Dhe-Paganon, S. / Duda, K. / Iwamoto, M. / Chi, Y.I. / Shoelson, S.E.
History
DepositionJul 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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

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Assembly

Deposited unit
A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
C: Hepatocyte nuclear factor 4-alpha
D: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2838
Polymers112,4824
Non-polymers8014
Water1,33374
1
A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6424
Polymers56,2412
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Hepatocyte nuclear factor 4-alpha
D: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6424
Polymers56,2412
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint2 kcal/mol
Surface area21390 Å2
MethodPISA
3
A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
C: Hepatocyte nuclear factor 4-alpha
D: Hepatocyte nuclear factor 4-alpha
hetero molecules

A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
C: Hepatocyte nuclear factor 4-alpha
D: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,56616
Polymers224,9648
Non-polymers1,6038
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area26590 Å2
ΔGint-80 kcal/mol
Surface area73340 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-12 kcal/mol
Surface area41020 Å2
MethodPISA
5
A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
hetero molecules

C: Hepatocyte nuclear factor 4-alpha
D: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2838
Polymers112,4824
Non-polymers8014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8800 Å2
ΔGint-10 kcal/mol
Surface area41170 Å2
MethodPISA
6
B: Hepatocyte nuclear factor 4-alpha
C: Hepatocyte nuclear factor 4-alpha
hetero molecules

B: Hepatocyte nuclear factor 4-alpha
C: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2838
Polymers112,4824
Non-polymers8014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10670 Å2
ΔGint-45 kcal/mol
Surface area41190 Å2
MethodPISA
7
B: Hepatocyte nuclear factor 4-alpha
hetero molecules

C: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6424
Polymers56,2412
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2930 Å2
ΔGint-5 kcal/mol
Surface area23010 Å2
MethodPISA
8
B: Hepatocyte nuclear factor 4-alpha
C: Hepatocyte nuclear factor 4-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6424
Polymers56,2412
Non-polymers4012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-2 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.288, 102.288, 227.688
Angle α, β, γ (deg.)90, 90, 90
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: 28120.455 Da / Num. of mol.: 4 / Fragment: Residues 133-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / Gene: HNF4a / Plasmid: pet28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22449
#2: Chemical
ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
20.1 Msodium citrate1reservoirpH8.0
30.7 Mammonium acetate1reservoir
416 %MPD1reservoir
510 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: BRANDEIS - B1.2 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 29727 / Observed criterion σ(I): 0.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å /
RfactorNum. reflection
Rfree0.282 -
Rwork0.237 -
obs-29727
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7050 0 56 74 7180
Refinement
*PLUS
Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0078
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.35

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