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- PDB-4jgv: Crystal Structure of Human Nur77 Ligand-binding Domain in Complex... -

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Basic information

Entry
Database: PDB / ID: 4jgv
TitleCrystal Structure of Human Nur77 Ligand-binding Domain in Complex with THPN
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / cellular response to corticotropin-releasing hormone stimulus / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / skeletal muscle cell differentiation / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / apoptotic process / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear receptor / 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 ...Orphan nuclear receptor, HMR type / Orphan nuclear receptor / 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
1-(3,4,5-trihydroxyphenyl)nonan-1-one / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsZhang, Q. / Li, F. / Li, A. / Tian, X. / Wan, W. / Wan, Y. / Chen, H. / Xing, Y. / Wu, Q. / Lin, T.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Orphan nuclear receptor TR3 acts in autophagic cell death via mitochondrial signaling pathway.
Authors: Wang, W. / Wang, Y. / Chen, H. / Xing, Y. / Li, F. / Zhang, Q. / Zhou, B. / Zhang, H. / Zhang, J. / Bian, X. / Li, L. / Liu, Y. / Zhao, B. / Chen, Y. / Wu, R. / Li, A. / Yao, L. / Chen, P. / ...Authors: Wang, W. / Wang, Y. / Chen, H. / Xing, Y. / Li, F. / Zhang, Q. / Zhou, B. / Zhang, H. / Zhang, J. / Bian, X. / Li, L. / Liu, Y. / Zhao, B. / Chen, Y. / Wu, R. / Li, A. / Yao, L. / Chen, P. / Zhang, Y. / Tian, X. / Beermann, F. / Wu, M. / Han, J. / Huang, P. / Lin, T. / Wu, Q.
History
DepositionMar 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Nuclear receptor subfamily 4 group A member 1
B: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,17110
Polymers55,2602
Non-polymers9118
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-14 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.084, 76.900, 128.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 362 - 598 / Label seq-ID: 13 - 249

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Nuclear receptor subfamily 4 group A member 1 / Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR ...Early response protein NAK1 / Nuclear hormone receptor NUR/77 / Nur77 / Orphan nuclear receptor HMR / Orphan nuclear receptor TR3 / ST-59 / Testicular receptor 3


Mass: 27630.041 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, UNP residues 351-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1, GFRP1, HMR, NAK1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22736
#2: Chemical ChemComp-T94 / 1-(3,4,5-trihydroxyphenyl)nonan-1-one


Mass: 266.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.3 Å3/Da / Density % sol: 62.76 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 4.8
Details: 7% PEG 6000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, EVAPORATION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97924 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 28, 2012
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 15133 / Num. obs: 15103 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.103
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.4 % / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→49.3 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.362 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25587 757 5 %RANDOM
Rwork0.17791 ---
obs0.18175 14304 99.41 %-
all-14389 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0 Å2
2--0.92 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 3.01→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 61 216 3893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193743
X-RAY DIFFRACTIONr_bond_other_d0.0050.023733
X-RAY DIFFRACTIONr_angle_refined_deg1.4842.0135051
X-RAY DIFFRACTIONr_angle_other_deg1.07938599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8823.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75115653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0491528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214050
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02808
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13244 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.006→3.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 57 -
Rwork0.207 1020 -
obs--95.65 %

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