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- PDB-6kz5: Crystal Structure Analysis of the Csn-B-bounded NUR77 Ligand bind... -

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Basic information

Entry
Database: PDB / ID: 6kz5
TitleCrystal Structure Analysis of the Csn-B-bounded NUR77 Ligand binding Domain
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION / NR4A1 / Nur77
Function / homology
Function and homology information


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 / macrophage activation / cell migration involved in sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer ...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 / macrophage activation / cell migration involved in sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / fat cell differentiation / negative regulation of cell cycle / skeletal muscle cell differentiation / cellular response to vascular endothelial growth factor stimulus / cellular response to fibroblast growth factor stimulus / positive regulation of endothelial cell proliferation / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / fibrillar center / protein import into nucleus / sequence-specific double-stranded DNA binding / 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 / nuclear speck / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / protein heterodimerization activity / apoptotic process / regulation of transcription by RNA polymerase II / chromatin / 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 / 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 ...Orphan nuclear receptor, HMR type / Orphan nuclear receptor / 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
Chem-E4L / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.45 Å
AuthorsHong, W. / Chen, H. / Wu, Q. / Lin, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Blocking PPAR gamma interaction facilitates Nur77 interdiction of fatty acid uptake and suppresses breast cancer progression.
Authors: Yang, P.B. / Hou, P.P. / Liu, F.Y. / Hong, W.B. / Chen, H.Z. / Sun, X.Y. / Li, P. / Zhang, Y. / Ju, C.Y. / Luo, L.J. / Wu, S.F. / Zhou, J.X. / Wang, Z.J. / He, J.P. / Li, L. / Zhao, T.J. / ...Authors: Yang, P.B. / Hou, P.P. / Liu, F.Y. / Hong, W.B. / Chen, H.Z. / Sun, X.Y. / Li, P. / Zhang, Y. / Ju, C.Y. / Luo, L.J. / Wu, S.F. / Zhou, J.X. / Wang, Z.J. / He, J.P. / Li, L. / Zhao, T.J. / Deng, X. / Lin, T. / Wu, Q.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Blocking PPAR gamma interaction facilitates Nur77 interdiction of fatty acid uptake and suppresses breast cancer progression
Authors: Yang, P. / Hou, P. / Liu, F. / Hong, W. / Chen, H. / Sun, X. / Li, P. / Zhang, Y. / Ju, C. / Luo, L. / Wu, S. / Zhou, J. / Wang, Z. / He, J. / Li, L. / Zhao, T. / Deng, X. / Lin, T. / Wu, Q.
#2: Journal: Nat. Chem. Biol. / Year: 2012
Title: The orphan nuclear receptor Nur77 regulates LKB1 localization and activates AMPK.
Authors: Zhan, Y.Y. / Chen, Y. / Zhang, Q. / Zhuang, J.J. / Tian, M. / Chen, H.Z. / Zhang, L.R. / Zhang, H.K. / He, J.P. / Wang, W.J. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A.Z. / Xin, Y.Z. / ...Authors: Zhan, Y.Y. / Chen, Y. / Zhang, Q. / Zhuang, J.J. / Tian, M. / Chen, H.Z. / Zhang, L.R. / Zhang, H.K. / He, J.P. / Wang, W.J. / Wu, R. / Wang, Y. / Shi, C. / Yang, K. / Li, A.Z. / Xin, Y.Z. / Li, T.Y. / Yang, J.Y. / Zheng, Z.H. / Yu, C.D. / Lin, S.C. / Chang, C. / Huang, P.Q. / Lin, T. / Wu, Q.
History
DepositionSep 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)57,8133
Polymers57,4912
Non-polymers3221
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-16 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.589, 76.099, 127.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 28745.305 Da / Num. of mol.: 2
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-E4L / ethyl 2-[2-octanoyl-3,5-bis(oxidanyl)phenyl]ethanoate / ethyl 2-(3,5-dihydroxy-2-octanoylphenyl)acetate


Mass: 322.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26O5 / Feature type: SUBJECT OF INVESTIGATION
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: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Crystals of apo-LBD was obtained at 4 degrees Celsius by hanging drop vapor diffusion. The droplets consisted of a 1:1 (v/v) mixture of LBD at 6 mg/ml, and the well solution consisted of 100 ...Details: Crystals of apo-LBD was obtained at 4 degrees Celsius by hanging drop vapor diffusion. The droplets consisted of a 1:1 (v/v) mixture of LBD at 6 mg/ml, and the well solution consisted of 100 mM sodium citrate (pH 4.6), 22% glycerol and 5% PEG4000. Crystals appeared after 24-48 h and were ready for data collection in 7 d.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: SDMS / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4.45→50 Å / Num. obs: 4038 / % possible obs: 91.2 % / Redundancy: 2.4 % / CC1/2: 0.914 / Rmerge(I) obs: 0.149 / Net I/σ(I): 4.514
Reflection shellResolution: 4.5→4.58 Å / Rmerge(I) obs: 0.492 / Num. unique obs: 197 / CC1/2: 0.656

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3E

3v3e


Resolution: 4.45→33.28 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.745 / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3079 154 4.5 %RANDOM
Rwork0.2457 ---
obs0.2485 3241 70.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.17 Å2 / Biso mean: 27.911 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.28 Å20 Å20 Å2
2---0.4 Å20 Å2
3----7.88 Å2
Refinement stepCycle: final / Resolution: 4.45→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3634 0 23 0 3657
Biso mean--69.45 --
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133740
X-RAY DIFFRACTIONr_bond_other_d0.0110.0173635
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.6315066
X-RAY DIFFRACTIONr_angle_other_deg1.4341.578410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2421.202183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84115648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3731528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02783
LS refinement shellResolution: 4.45→4.562 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.224 3 -
Rwork0.224 168 -
obs--52.29 %

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