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- PDB-4b7w: Ligand binding domain human hepatocyte nuclear factor 4alpha: Apo form -

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Basic information

Entry
Database: PDB / ID: 4b7w
TitleLigand binding domain human hepatocyte nuclear factor 4alpha: Apo form
ComponentsHEPATOCYTE NUCLEAR FACTOR 4-ALPHA
KeywordsRECEPTOR / NUCLEAR RECEPTOR
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
Hepatocyte nuclear factor 4-alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsDudasova, Z. / Okvist, M. / Kretova, M. / Ondrovicova, G. / Skrabana, R. / LeGuevel, R. / Salbert, G. / Leonard, G. / McSweeney, S. / Barath, P.
CitationJournal: To be Published
Title: Fatty Acids are not Essential Structural Components of Hepatocyte Nuclear Factor 4Alpha
Authors: Dudasova, Z. / Okvist, M. / Kretova, M. / Ondrovicova, G. / Skrabana, R. / Leguevel, R. / Salbert, G. / Leonard, G. / Mcsweeney, S. / Barath, P.
History
DepositionAug 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
D: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA


Theoretical massNumber of molelcules
Total (without water)107,6854
Polymers107,6854
Non-polymers00
Water00
1
A: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
C: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
D: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA

A: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
B: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
C: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA
D: HEPATOCYTE NUCLEAR FACTOR 4-ALPHA


Theoretical massNumber of molelcules
Total (without water)215,3708
Polymers215,3708
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20960 Å2
ΔGint-124.4 kcal/mol
Surface area73520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.048, 105.282, 98.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.26544, 0.96413, -0.00102), (0.96404, 0.26543, 0.01294), (0.01274, 0.00245, -0.99992)0.16176, -0.84988, 52.36674
2given(-0.24881, 0.96855, -0.0025), (0.9682, 0.24879, 0.02635), (0.02614, 0.00414, -0.99965)0.25932, -1.20403, 52.34188

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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: 26921.195 Da / Num. of mol.: 4 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 142-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41235

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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: 2.83 Å3/Da / Density % sol: 56.6 % / Description: NONE
Crystal growpH: 8
Details: 0.7 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, 10 MM DTT, 16% MPD IN 0.1 M TRIS, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 6, 2009 / Details: KB MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 4→46.7 Å / Num. obs: 8011 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.1
Reflection shellResolution: 4→4.24 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.8 / % possible all: 89

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Processing

Software
NameClassification
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LV2

1lv2


Resolution: 4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: STRUCTURE REFINEMENT WAS CARRIED OUT USING THE CNS-DEN METHODOLOGY. SEE SCHRODER, G. F., LEVITT, M. & BRUNGER, A. T. 2010. SUPER-RESOLUTION BIOMOLECULAR CRYSTALLOGRAPHY WITH LOW-RESOLUTION ...Details: STRUCTURE REFINEMENT WAS CARRIED OUT USING THE CNS-DEN METHODOLOGY. SEE SCHRODER, G. F., LEVITT, M. & BRUNGER, A. T. 2010. SUPER-RESOLUTION BIOMOLECULAR CRYSTALLOGRAPHY WITH LOW-RESOLUTION DATA. NATURE 464, 1218-1222.
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 374 4 %RANDOM
Rwork0.2496 ---
obs0.2496 7987 85.9 %-
Solvent computationBsol: 111.407 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--40.406 Å20 Å20 Å2
2---10.376 Å20 Å2
3---50.781 Å2
Refinement stepCycle: LAST / Resolution: 4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6476 0 0 0 6476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.002477
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.65528
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 4→4.14 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 35 4 %
Rwork0.362 620 -
obs--73.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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