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- PDB-3fs1: Crystal structure of HNF4a LBD in complex with the ligand and the... -

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Basic information

Entry
Database: PDB / ID: 3fs1
TitleCrystal structure of HNF4a LBD in complex with the ligand and the coactivator PGC-1a fragment
Components
  • Hepatocyte nuclear factor 4-alpha
  • PPARgamma Coactivator-1a (PGC-1a)
KeywordsTRANSCRIPTION / Nuclear Receptor / Coactivator / LXXLL motif / MODY / Diabetes / Alternative promoter usage / Alternative splicing / Diabetes mellitus / Disease mutation / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Receptor / Transcription regulation / Zinc / Zinc-finger
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
: / : / 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 ...: / : / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsRha, G. / Wu, G. / Chi, Y.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Multiple binding modes between HNF4alpha and the LXXLL motifs of PGC-1alpha lead to full activation
Authors: Rha, G.B. / Wu, G. / Shoelson, S.E. / Chi, Y.I.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: Hepatocyte nuclear factor 4-alpha
B: PPARgamma Coactivator-1a (PGC-1a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0063
Polymers26,7772
Non-polymers2281
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-7 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.049, 113.049, 57.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Hepatocyte nuclear factor 4-alpha / 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: 25993.256 Da / Num. of mol.: 1 / Fragment: HNF4a Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4, HNF4A, NR2A1, TCF14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41235
#2: Protein/peptide PPARgamma Coactivator-1a (PGC-1a)


Mass: 783.955 Da / Num. of mol.: 1 / Fragment: PGC-1a LXXLL motifs
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGC-1a / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MYR / MYRISTIC ACID


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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.42 Å3/Da / Density % sol: 64.03 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 14, 2008
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR HIGH-RESOLUTION DOUBLE-CRYSTAL SI (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40.2 Å / Num. all: 19035 / Num. obs: 18995 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 29.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.56 / Num. unique all: 1636 / Rsym value: 0.349 / % possible all: 87

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.506 / Cor.coef. Fo:Fc: 0.601
Highest resolutionLowest resolution
Rotation3 Å46.51 Å
Translation3 Å46.51 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PZL (without the ligand and the peptide)

1pzl


Resolution: 2.2→40 Å / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU R Cruickshank DPI: 0.19 / SU Rfree: 0.176 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.236 922 -
Rwork0.19 --
obs0.195 18017 98.2 %
all-18017 -
Displacement parametersBiso max: 81.18 Å2 / Biso mean: 35.477 Å2 / Biso min: 11.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2--2.43 Å20 Å2
3----4.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.28 Å
Luzzati d res low-10 Å
Luzzati sigma a0.25 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 16 77 1973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.036
X-RAY DIFFRACTIONc_angle_deg2.444
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d2.59

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