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- PDB-8c1l: Crystal structure of HNF4 alpha LBD in complexes with palmitic ac... -

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Basic information

Entry
Database: PDB / ID: 8c1l
TitleCrystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide
Components
  • Hepatocyte nuclear factor 4-alpha
  • Nuclear receptor coactivator 2
KeywordsDNA BINDING PROTEIN / complex
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / lipid homeostasis ...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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / lipid homeostasis / locomotor rhythm / Regulation of gene expression in beta cells / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to glucose / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / positive regulation of adipose tissue development / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of insulin secretion / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / fatty acid binding / nuclear receptor binding / negative regulation of smoothened signaling pathway / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / Heme signaling / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / regulation of circadian rhythm / negative regulation of cell growth / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / lipid metabolic process / RNA polymerase II transcription regulator complex / nuclear receptor activity / : / blood coagulation / sequence-specific double-stranded DNA binding / rhythmic process / glucose homeostasis / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / 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 coactivator activity / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / signaling receptor binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
PALMITIC ACID / Hepatocyte nuclear factor 4-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNi, X. / Merk, D. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide
Authors: Ni, X. / Merk, D. / Zhubi, R. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionDec 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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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: Hepatocyte nuclear factor 4-alpha
D: Nuclear receptor coactivator 2
E: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4459
Polymers54,7464
Non-polymers6995
Water1,62190
1
A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
D: Nuclear receptor coactivator 2
hetero molecules

E: Nuclear receptor coactivator 2


Theoretical massNumber of molelcules
Total (without water)55,4459
Polymers54,7464
Non-polymers6995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Unit cell
Length a, b, c (Å)57.277, 82.457, 57.360
Angle α, β, γ (deg.)90.00, 111.84, 90.00
Int Tables number4
Space group name H-MP1211

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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: 26211.529 Da / Num. of mol.: 2
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 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1161.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 284 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 -- 10% ethylene glycol -- 0.1M bis-tris-propane pH 8.5 -- 0.2M sodium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.37 Å / Num. obs: 32417 / % possible obs: 97 % / Redundancy: 5.2 % / CC1/2: 0.999 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2491 / CC1/2: 0.822

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 11.098 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23667 1591 4.9 %RANDOM
Rwork0.19534 ---
obs0.19733 30802 96.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.775 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å21.66 Å2
2---2.09 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3509 0 48 90 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133605
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153615
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.634856
X-RAY DIFFRACTIONr_angle_other_deg1.2511.5768296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.41322.541181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92315651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5521524
X-RAY DIFFRACTIONr_chiral_restr0.0610.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023967
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02777
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1022.9581777
X-RAY DIFFRACTIONr_mcbond_other2.0942.9561776
X-RAY DIFFRACTIONr_mcangle_it2.94.4112209
X-RAY DIFFRACTIONr_mcangle_other2.9014.4142210
X-RAY DIFFRACTIONr_scbond_it2.7063.2671828
X-RAY DIFFRACTIONr_scbond_other2.7063.2691829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0654.7762647
X-RAY DIFFRACTIONr_long_range_B_refined5.78335.673996
X-RAY DIFFRACTIONr_long_range_B_other5.78435.6863997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6608 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 115 -
Rwork0.289 2372 -
obs--99.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9879-0.3098-1.84642.81330.8553.1134-0.0252-0.21240.0190.24630.1042-0.56010.090.413-0.0790.15970.0063-0.01590.12040.00580.145418.660912.361619.0676
21.25970.67570.63184.07710.08921.18480.0160.2156-0.3306-0.07530.0705-0.52010.10110.1301-0.08650.14870.04470.06690.099-0.03090.146514.81490.73779.3737
35.89680.04171.49966.31912.14033.4599-0.03460.29280.4162-0.22590.106-0.4454-0.35750.3762-0.07130.2398-0.02190.0510.1470.02990.169916.549425.438112.2692
48.8981-3.51052.570816.1161-3.398511.06140.0256-0.2113-0.5209-0.1471-0.2186-0.25090.61240.17620.1930.2099-0.02530.02530.2147-0.04670.2565-3.2808-4.1665-13.3094
52.0250.1822-0.87761.6204-0.69332.96860.02630.0259-0.1635-0.1193-0.04710.08210.09290.0570.02080.1389-0.00820.06340.0101-0.020.06945.31475.797-10.4289
62.4439-2.49081.434.5911-1.65121.20560.0011-0.17030.1381-0.0896-0.05730.1843-0.01430.05370.05620.1824-0.0030.08910.0872-0.04580.11985.717517.2811-7.2047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 252
2X-RAY DIFFRACTION2A253 - 339
3X-RAY DIFFRACTION3A340 - 368
4X-RAY DIFFRACTION4B141 - 154
5X-RAY DIFFRACTION5B166 - 324
6X-RAY DIFFRACTION6B325 - 368

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