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- PDB-9m2e: Crystal Structure of Nur77 LBD in complex with DBIC compound -

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Basic information

Entry
Database: PDB / ID: 9m2e
TitleCrystal Structure of Nur77 LBD in complex with DBIC compound
ComponentsNuclear receptor subfamily 4immunitygroup A member 1
KeywordsTRANSCRIPTION / complex
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
: / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.575 Å
AuthorsHong, W.B. / Lin, T.W. / Chen, X.Q. / Wu, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of Nur77 LBD in complex with DBIC compound
Authors: Wu, L.Z. / Hong, W.B.
History
DepositionFeb 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BBB: Nuclear receptor subfamily 4immunitygroup A member 1
AAA: Nuclear receptor subfamily 4immunitygroup A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4163
Polymers55,0862
Non-polymers3301
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-14 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.522, 76.094, 128.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11BBB
21AAA

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 362 - 598 / Label seq-ID: 12 - 248

Dom-IDAuth asym-IDLabel asym-ID
1BBBA
2AAAB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Nuclear receptor subfamily 4immunitygroup 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: 27542.963 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-A1D7W / dodecyl 1H-benzimidazole-5-carboxylate


Mass: 330.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 62.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG4000, Sodium citrate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 22762 / % possible obs: 95.8 % / Redundancy: 3.1 % / CC1/2: 0.78 / Net I/σ(I): 11.867
Reflection shellResolution: 2.57→2.61 Å / Num. unique obs: 22762 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.575→33.36 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.895 / SU B: 10.339 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / ESU R: 0.43 / ESU R Free: 0.3
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2655 1075 4.881 %
Rwork0.2062 20948 -
all0.209 --
obs-22023 92.674 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.735 Å2
Baniso -1Baniso -2Baniso -3
1-0.478 Å20 Å20 Å2
2--0.196 Å2-0 Å2
3----0.674 Å2
Refinement stepCycle: LAST / Resolution: 2.575→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3582 0 24 95 3701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133679
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153640
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.6294975
X-RAY DIFFRACTIONr_angle_other_deg1.2291.5748387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25621.16181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.84515647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5241528
X-RAY DIFFRACTIONr_chiral_restr0.0690.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02816
X-RAY DIFFRACTIONr_nbd_refined0.2120.2832
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23285
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21818
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21876
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2129
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.214
X-RAY DIFFRACTIONr_nbd_other0.2430.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1990.24
X-RAY DIFFRACTIONr_mcbond_it3.2484.3481819
X-RAY DIFFRACTIONr_mcbond_other3.2424.3471818
X-RAY DIFFRACTIONr_mcangle_it5.1396.5012265
X-RAY DIFFRACTIONr_mcangle_other5.1386.5032266
X-RAY DIFFRACTIONr_scbond_it3.5014.6721860
X-RAY DIFFRACTIONr_scbond_other3.54.6741861
X-RAY DIFFRACTIONr_scangle_it5.5936.8572710
X-RAY DIFFRACTIONr_scangle_other5.5926.8582711
X-RAY DIFFRACTIONr_lrange_it10.13280.57615193
X-RAY DIFFRACTIONr_lrange_other10.12480.60415173
X-RAY DIFFRACTIONr_ncsr_local_group_10.1370.056774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BBBX-RAY DIFFRACTIONLocal ncs0.136970.05006
12AAAX-RAY DIFFRACTIONLocal ncs0.136970.05006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.575-2.6420.268530.2751204X-RAY DIFFRACTION73.0814
2.642-2.7140.296790.2711332X-RAY DIFFRACTION83.7886
2.714-2.7930.33730.2451390X-RAY DIFFRACTION89.4801
2.793-2.8780.33720.2521446X-RAY DIFFRACTION95.0532
2.878-2.9730.342670.2381417X-RAY DIFFRACTION95.8037
2.973-3.0770.305860.2141342X-RAY DIFFRACTION96.4213
3.077-3.1930.26860.211306X-RAY DIFFRACTION96.3989
3.193-3.3230.324580.2071310X-RAY DIFFRACTION97.4359
3.323-3.470.295600.21249X-RAY DIFFRACTION97.2511
3.47-3.6390.21670.1951178X-RAY DIFFRACTION97.7237
3.639-3.8350.277350.1971144X-RAY DIFFRACTION96.3235
3.835-4.0670.262510.1921069X-RAY DIFFRACTION96.3027
4.067-4.3460.268680.182976X-RAY DIFFRACTION95.7798
4.346-4.6930.259470.168940X-RAY DIFFRACTION95.547
4.693-5.1380.242440.173862X-RAY DIFFRACTION94.7699
5.138-5.740.262440.204769X-RAY DIFFRACTION93.9884
5.74-6.620.23320.225687X-RAY DIFFRACTION93.8642
6.62-8.0870.253230.215595X-RAY DIFFRACTION92.6537
8.087-11.350.184200.157464X-RAY DIFFRACTION91.1488
11.35-33.360.148100.289265X-RAY DIFFRACTION82.8313

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