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- PDB-9ibr: Crystal structure of HNF4 alpha LBD complexed with GRIP-1 peptide... -

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Basic information

Entry
Database: PDB / ID: 9ibr
TitleCrystal structure of HNF4 alpha LBD complexed with GRIP-1 peptide and ESY13
Components
  • Hepatocyte nuclear factor 4-alpha
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Hepatocyte nuclear factor 4-alpha / Nuclear receptor
Function / homology
Function and homology information


regulation of growth hormone receptor signaling pathway / regulation of 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 / regulation of 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 lipid metabolic process / response to glucose / regulation of insulin secretion / xenobiotic metabolic process / cholesterol homeostasis / fatty acid binding / regulation of circadian rhythm / negative regulation of cell growth / Nuclear Receptor transcription pathway / lipid metabolic process / nuclear receptor activity / blood coagulation / sequence-specific double-stranded DNA binding / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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
: / : / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...: / : / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
Similarity search - Domain/homology
: / Hepatocyte nuclear factor 4-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsMorozov, V. / Merk, D. / Schallmayer, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: A First-in-Class Hepatocyte Nuclear Factor 4 Agonist.
Authors: Schallmayer, E. / Morozov, V. / Duensing-Kropp, S. / Schallmayer, L. / Schuffner, L. / Schubert-Zsilavecz, M. / Pabel, J. / Hofner, G. / Heering, J. / Marschner, J.A. / Merk, D.
History
DepositionFeb 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatocyte nuclear factor 4-alpha
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5073
Polymers27,2702
Non-polymers2371
Water00
1
A: Hepatocyte nuclear factor 4-alpha
B: Nuclear receptor coactivator 2
hetero molecules

A: Hepatocyte nuclear factor 4-alpha
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0146
Polymers54,5404
Non-polymers4742
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Unit cell
Length a, b, c (Å)87.769, 87.769, 62.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Hepatocyte nuclear factor 4-alpha / HNF-4-alpha / Nuclear receptor subfamily 2 group A member 1 / Transcription factor 14 / TCF-14 / ...HNF-4-alpha / Nuclear receptor subfamily 2 group A member 1 / Transcription factor 14 / TCF-14 / Transcription factor HNF-4


Mass: 25993.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4A, HNF4, NR2A1, TCF14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41235
#2: Protein/peptide Nuclear receptor coactivator 2


Mass: 1276.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-A1I1W / 2-hydroxy-5-(phenylethynyl)benzoic acid


Mass: 237.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H9O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG3350 8% ethylene glycol 0.1M bis-tris-propane pH 8.5 -

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.13→51.12 Å / Num. obs: 4630 / % possible obs: 92.5 % / Redundancy: 2.69 % / CC1/2: 0.997 / Net I/σ(I): 6.1
Reflection shellResolution: 2.777→3.031 Å / Num. unique obs: 231 / CC1/2: 0.103

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
STARANISOdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
autoPROCdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→51.12 Å / SU ML: 0.4001 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.8201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3546 245 5.29 %
Rwork0.2898 4384 -
obs0.2923 4629 70.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.54 Å2
Refinement stepCycle: LAST / Resolution: 2.78→51.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 18 0 1699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211718
X-RAY DIFFRACTIONf_angle_d1.52232327
X-RAY DIFFRACTIONf_chiral_restr0.0777281
X-RAY DIFFRACTIONf_plane_restr0.0094301
X-RAY DIFFRACTIONf_dihedral_angle_d18.8319604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-3.50.3931800.36271170X-RAY DIFFRACTION38.92
3.5-51.120.34771650.27843214X-RAY DIFFRACTION99.94

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