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- PDB-4iqr: Multi-Domain Organization of the HNF4alpha Nuclear Receptor Compl... -

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Basic information

Entry
Database: PDB / ID: 4iqr
TitleMulti-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA
Components
  • DNA (5'-D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3')
  • DNA (5'-D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
  • Hepatocyte nuclear factor 4-alpha
  • Nuclear receptor coactivator 2
KeywordsTranscription/DNA / Transcription Factor / Transcription-DNA complex
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 / triglyceride homeostasis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / lipid homeostasis ...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 / triglyceride homeostasis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / lipid homeostasis / locomotor rhythm / Regulation of gene expression in beta cells / regulation of insulin secretion / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / 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 / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / response to progesterone / cholesterol homeostasis / fatty acid binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / lipid metabolic process / negative regulation of cell growth / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / rhythmic process / blood coagulation / Circadian Clock / sequence-specific double-stranded DNA binding / glucose homeostasis / 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 / nuclear body / protein dimerization activity / 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 / protein domain specific binding / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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
: / : / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 ...: / : / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MYRISTIC ACID / DNA / DNA (> 10) / Hepatocyte nuclear factor 4-alpha / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChandra, V. / Huang, P. / Kim, Y. / Rastinejad, F.
CitationJournal: Nature / Year: 2013
Title: Multidomain integration in the structure of the HNF-4 alpha nuclear receptor complex.
Authors: Chandra, V. / Huang, P. / Potluri, N. / Wu, D. / Kim, Y. / Rastinejad, F.
History
DepositionJan 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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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
C: DNA (5'-D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
D: DNA (5'-D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3')
E: Hepatocyte nuclear factor 4-alpha
F: Hepatocyte nuclear factor 4-alpha
G: DNA (5'-D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
H: DNA (5'-D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3')
I: Nuclear receptor coactivator 2
J: Nuclear receptor coactivator 2
K: Nuclear receptor coactivator 2
L: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,73124
Polymers185,29412
Non-polymers1,43712
Water0
1
A: Hepatocyte nuclear factor 4-alpha
B: Hepatocyte nuclear factor 4-alpha
C: DNA (5'-D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
D: DNA (5'-D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3')
I: Nuclear receptor coactivator 2
J: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,36512
Polymers92,6476
Non-polymers7186
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12330 Å2
ΔGint-44 kcal/mol
Surface area35780 Å2
MethodPISA
2
E: Hepatocyte nuclear factor 4-alpha
F: Hepatocyte nuclear factor 4-alpha
G: DNA (5'-D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')
H: DNA (5'-D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3')
K: Nuclear receptor coactivator 2
L: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,36512
Polymers92,6476
Non-polymers7186
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-42 kcal/mol
Surface area36100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.786, 57.596, 166.305
Angle α, β, γ (deg.)90.00, 96.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules CGDH

#2: DNA chain DNA (5'-D(*GP*GP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3')


Mass: 6232.056 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*GP*TP*TP*C)-3')


Mass: 6035.902 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein / Protein/peptide , 2 types, 8 molecules ABEFIJKL

#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: 38567.598 Da / Num. of mol.: 4 / Fragment: unp residues 55-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNF4A, HNF4, NR2A1, TCF14 / Production host: Escherichia coli (E. coli) / References: UniProt: P41235
#4: Protein/peptide
Nuclear receptor coactivator 2 / / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1621.902 Da / Num. of mol.: 4 / Fragment: LxxLL motif peptide (unp residues 685-697) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596

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Non-polymers , 2 types, 12 molecules

#5: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 25mM NH4Cl, 25mM MgCl2 and PEG 3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 51050 / Num. obs: 50948 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rsym value: 0.083 / Net I/σ(I): 20.3
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.688 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
CNS1.3refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 3FS1 and 3CBB

3fs1

3cbb


Resolution: 2.9→48.81 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2559 -RANDOM
Rwork0.239 ---
all0.241 50811 --
obs0.241 50589 99.5 %-
Displacement parametersBiso mean: 87.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.75 Å20 Å2-19.39 Å2
2---5.22 Å20 Å2
3----5.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10083 1628 72 0 11783
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.393 435 -
Rwork0.354 --
obs-8355 99.7 %

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