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- PDB-4rzf: Crystal Structure Analysis of the NUR77 Ligand Binding Domain, S4... -

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Basic information

Entry
Database: PDB / ID: 4rzf
TitleCrystal Structure Analysis of the NUR77 Ligand Binding Domain, S441W mutant
ComponentsNuclear receptor subfamily 4 group A member 1
KeywordsTRANSCRIPTION
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 / fibrillar center / nuclear receptor activity / 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 / Retinoid X Receptor / Retinoid X 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 ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLi, F. / Tian, X. / Li, A. / Li, L. / Liu, Y. / Chen, H. / Wu, Q. / Lin, T.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Impeding the interaction between Nur77 and p38 reduces LPS-induced inflammation.
Authors: Li, L. / Liu, Y. / Chen, H.Z. / Li, F.W. / Wu, J.F. / Zhang, H.K. / He, J.P. / Xing, Y.Z. / Chen, Y. / Wang, W.J. / Tian, X.Y. / Li, A.Z. / Zhang, Q. / Huang, P.Q. / Han, J. / Lin, T. / Wu, Q.
History
DepositionDec 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 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
B: Nuclear receptor subfamily 4 group A member 1
A: Nuclear receptor subfamily 4 group A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7035
Polymers57,4262
Non-polymers2763
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-15 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.542, 76.183, 128.095
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
11B
21A

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: 31 - 267 / Label seq-ID: 12 - 248

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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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: 28713.242 Da / Num. of mol.: 2 / Fragment: Nur77-LBD / Mutation: S441W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFRP1, HMR, NAK1, NR4A1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22736
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.17 Å3/Da / Density % sol: 61.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.2
Details: PEG4000, Sodium citrate, Glycerol, pH 4.2, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 3, 2014
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 43304 / % possible obs: 91.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.03-2.0730.341186.3
2.07-2.130.281191.9
2.1-2.143.10.255191.6
2.14-2.193.10.232192.3
2.19-2.233.10.204193.3
2.23-2.293.10.178193
2.29-2.343.10.162193.7
2.34-2.413.10.148193.9
2.41-2.483.20.131193.8
2.48-2.563.30.118194.3
2.56-2.653.40.108194.2
2.65-2.763.40.096193.8
2.76-2.883.50.086194.2
2.88-3.033.60.077194
3.03-3.223.70.071192.6
3.22-3.473.80.061192.9
3.47-3.823.80.063191.6
3.82-4.373.80.064189.8
4.37-5.513.70.052188.8
5.51-503.80.049182.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→33.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.237 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1668 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22732 2259 4.8 %RANDOM
Rwork0.18589 ---
obs0.18787 -93.38 %-
all-47120 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.431 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.99→33.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 18 342 4028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193764
X-RAY DIFFRACTIONr_bond_other_d0.0070.023729
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.9975094
X-RAY DIFFRACTIONr_angle_other_deg1.52338583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95823.165158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34415656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.671528
X-RAY DIFFRACTIONr_chiral_restr0.160.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214127
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02837
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_it3.953.7661856
X-RAY DIFFRACTIONr_mcbond_other3.953.7651855
X-RAY DIFFRACTIONr_mcangle_it5.335.6052313
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9024.1521908
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 13266 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 154 -
Rwork0.248 3111 -
obs--88.92 %

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