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- PDB-6l6q: Structural basis of NR4A2 homodimers binding to selective Nur-res... -

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Basic information

Entry
Database: PDB / ID: 6l6q
TitleStructural basis of NR4A2 homodimers binding to selective Nur-responsive elements
Components
  • DNA (5'-D(P*AP*GP*TP*GP*AP*CP*CP*TP*TP*TP*AP*AP*AP*GP*GP*TP*CP*AP*CP*T)-3')
  • Nuclear receptor related 1
KeywordsDNA BINDING PROTEIN / NR4A2 / nuclear receptor
Function / homology
Function and homology information


general adaptation syndrome / habenula development / central nervous system neuron differentiation / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / regulation of dopamine metabolic process / : / midbrain dopaminergic neuron differentiation / nuclear glucocorticoid receptor binding / regulation of respiratory gaseous exchange ...general adaptation syndrome / habenula development / central nervous system neuron differentiation / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / regulation of dopamine metabolic process / : / midbrain dopaminergic neuron differentiation / nuclear glucocorticoid receptor binding / regulation of respiratory gaseous exchange / dopaminergic neuron differentiation / neuron maturation / dopamine biosynthetic process / positive regulation of catalytic activity / fat cell differentiation / negative regulation of apoptotic signaling pathway / canonical Wnt signaling pathway / nuclear retinoid X receptor binding / response to amphetamine / adult locomotory behavior / post-embryonic development / neuron migration / SUMOylation of intracellular receptors / beta-catenin binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / negative regulation of neuron apoptotic process / transcription regulator complex / transcription by RNA polymerase II / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Orphan nuclear receptor, NURR type / Orphan nuclear receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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, NURR type / Orphan nuclear receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear receptor subfamily 4 group A member 2 / Nuclear receptor subfamily 4 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsJiang, L. / Chen, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China81372904 and 81570537 China
National Natural Science Foundation of China81272971 China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural basis of binding of homodimers of the nuclear receptor NR4A2 to selective Nur-responsive DNA elements.
Authors: Jiang, L. / Dai, S. / Li, J. / Liang, X. / Qu, L. / Chen, X. / Guo, M. / Chen, Z. / Chen, L. / Wei, H. / Chen, Y.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor related 1
B: Nuclear receptor related 1
C: DNA (5'-D(P*AP*GP*TP*GP*AP*CP*CP*TP*TP*TP*AP*AP*AP*GP*GP*TP*CP*AP*CP*T)-3')
F: DNA (5'-D(P*AP*GP*TP*GP*AP*CP*CP*TP*TP*TP*AP*AP*AP*GP*GP*TP*CP*AP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9218
Polymers31,6594
Non-polymers2624
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-32 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.696, 35.696, 259.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 262 through 329 or (resid 330...
21chain B
12chain C
22chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUVALVAL(chain A and (resid 262 through 329 or (resid 330...AA262 - 3291 - 68
121LYSLYSLYSLYS(chain A and (resid 262 through 329 or (resid 330...AA33069
131LEULEUPROPRO(chain A and (resid 262 through 329 or (resid 330...AA262 - 3461 - 85
141LEULEUPROPRO(chain A and (resid 262 through 329 or (resid 330...AA262 - 3461 - 85
151LEULEUPROPRO(chain A and (resid 262 through 329 or (resid 330...AA262 - 3461 - 85
161LEULEUPROPRO(chain A and (resid 262 through 329 or (resid 330...AA262 - 3461 - 85
211LEULEUPROPROchain BBB262 - 3461 - 85
112DADADTDTchain CCC1 - 201 - 20
212DADADTDTchain FFD1 - 201 - 20

NCS ensembles :
ID
1
2

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Components

#1: Protein Nuclear receptor related 1 / Nuclear receptor subfamily 4 group A member 2 isoform 1


Mass: 9696.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D8N6, UniProt: P43354*PLUS
#2: DNA chain DNA (5'-D(P*AP*GP*TP*GP*AP*CP*CP*TP*TP*TP*AP*AP*AP*GP*GP*TP*CP*AP*CP*T)-3')


Mass: 6132.991 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 150 mM NaCl, 50 mM MES (pH 5.93), 10 mM MgCl2, 5 mM CaCl2, and 10-12% PEG4K (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.601→32.41 Å / Num. obs: 9915 / % possible obs: 99.95 % / Redundancy: 13.8 % / CC1/2: 1 / Rmerge(I) obs: 0.07458 / Rrim(I) all: 0.07746 / Net I/σ(I): 16.81
Reflection shellResolution: 2.601→2.693 Å / Rmerge(I) obs: 0.5555 / Mean I/σ(I) obs: 4.42 / Num. unique obs: 990 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CIT

1cit


Resolution: 2.601→32.409 Å / Cross valid method: THROUGHOUT / σ(F): 99.69 / Phase error: 35.15
RfactorNum. reflection% reflection
Rfree0.2892 987 9.96 %
Rwork0.249 --
obs0.2553 9911 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.91 Å2 / Biso mean: 53.0539 Å2 / Biso min: 30.02 Å2
Refinement stepCycle: final / Resolution: 2.601→32.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 820 4 21 2172
Biso mean--42.66 39.31 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062261
X-RAY DIFFRACTIONf_angle_d0.8663202
X-RAY DIFFRACTIONf_chiral_restr0.047349
X-RAY DIFFRACTIONf_plane_restr0.004276
X-RAY DIFFRACTIONf_dihedral_angle_d18.6251232
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A776X-RAY DIFFRACTION8.499TORSIONAL
12B776X-RAY DIFFRACTION8.499TORSIONAL
21C394X-RAY DIFFRACTION8.499TORSIONAL
22F394X-RAY DIFFRACTION8.499TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 90 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6018-2.73880.39481480.415713081456
2.7388-2.91010.4161310.370612331364
2.9101-3.13440.36281460.347512791425
3.1344-3.4490.30571440.250112521396
3.449-3.94620.29221460.245312921438
3.9462-4.96480.25821380.210212701408
4.9648-24.22970.22371340.192112721406
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54250.2946-0.23490.505-0.06480.63970.00510.1151-0.0132-0.05740.0377-0.0358-0.05150.0534-0.00650.8358-0.33350.04410.7495-0.08310.199442.7352-21.0774-17.8937
20.1986-0.02170.18870.41770.09240.5239-0.02630.1041-0.0570.03260.1222-0.08510.08050.2607-0.07640.6912-0.120.09480.5645-0.13230.221744.7794-26.9194-8.1846
30.1769-0.2038-0.06350.74440.06820.02270.0244-0.13990.01320.1708-0.0376-0.0653-0.05420.0653-0.0050.9035-0.5650.07591.06940.12460.685155.0808-9.3536-21.7231
45.03650.942-1.61861.9071-2.34616.06180.0357-0.03390.06750.1218-0.010.082-0.0083-0.055-0.00360.6252-0.2933-0.25030.61360.1950.463261.3944-1.1472-44.3659
50.12680.07870.19570.05520.13410.32780.0504-0.1518-0.0530.1620.0112-0.05670.0861-0.0313-0.04880.7345-0.3605-0.1670.63310.1040.268457.3442-8.2455-41.7097
60.69690.0121-0.60650.2118-0.17251.24760.02090.1206-0.05190.035-0.020.00570.2364-0.08380.00040.5297-0.3117-0.06290.83030.02170.269756.4136-11.1863-56.3199
71.0295-0.6375-0.3621.47280.95191.2910.09410.1122-0.0405-0.16240.054-0.18750.03540.1353-0.10670.424-0.01180.05720.7390.06870.437765.0868-1.5492-56.9333
80.9022-0.3660.35871.3934-0.76190.55410.0970.1576-0.1201-0.0287-0.0753-0.16770.2260.1798-0.04530.7136-0.145-0.20210.71790.21170.500863.4211-11.0955-54.3288
91.77210.7522-1.05551.8809-0.63180.6509-0.17410.1744-0.2197-0.02810.01620.18830.2217-0.14910.10361.0435-0.4983-0.09620.80060.0910.421551.9357-19.8052-46.096
100.1153-0.00360.44040.0029-0.02261.86450.01570.07480.0065-0.05370.00060.05120.0695-0.0019-0.02060.7313-0.40130.06040.67130.08820.698443.6508-16.9815-39.2791
110.8038-0.2312-0.64681.09620.00732.32610.02310.0228-0.0130.0263-0.04220.01030.0962-0.10360.03120.5571-0.17930.09490.71870.05770.037748.9782-2.5966-56.3118
120.16170.0228-0.12060.071-0.17520.53820.01880.02010.06020.01580.02380.0188-0.0179-0.06590.0061.0099-0.51120.14351.13490.0729-0.268143.4034-8.4817-31.401
131.0861-0.62780.55810.79050.65592.5226-0.08390.15770.1834-0.2118-0.0427-0.0364-0.31250.06660.02830.7739-0.0659-0.13030.45480.06140.1134.1454-6.7595-8.4263
140.9088-0.1449-0.06750.7521-0.69371.8818-0.0457-0.0213-0.00610.04840.0156-0.0222-0.06890.08160.02640.6844-0.1650.1190.50420.1398-0.003738.3135-13.3006-8.0015
150.07460.1354-0.29180.5828-0.68731.2240.02640.04160.0511-0.04040.07580.032-0.1467-0.0143-0.08490.8207-0.35020.13260.74110.06560.104440.6673-5.6467-24.331
160.3221-0.10450.16940.4265-0.16971.9315-0.02170.0617-0.01460.0222-0.04-0.05560.10630.12180.07040.7717-0.3946-0.03440.76420.1754-0.323847.3477-9.6796-40.9496
170.7692-0.74960.48681.26390.4721.9852-0.0433-0.1516-0.0560.1711-0.07270.1730.0628-0.23350.01990.5041-0.04150.15610.7907-0.04650.163642.45251.5585-55.8166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 262 through 292 )A262 - 292
2X-RAY DIFFRACTION2chain 'A' and (resid 293 through 332 )A293 - 332
3X-RAY DIFFRACTION3chain 'A' and (resid 333 through 346 )A333 - 346
4X-RAY DIFFRACTION4chain 'B' and (resid 262 through 271 )B262 - 271
5X-RAY DIFFRACTION5chain 'B' and (resid 272 through 280 )B272 - 280
6X-RAY DIFFRACTION6chain 'B' and (resid 281 through 302 )B281 - 302
7X-RAY DIFFRACTION7chain 'B' and (resid 303 through 315 )B303 - 315
8X-RAY DIFFRACTION8chain 'B' and (resid 316 through 326 )B316 - 326
9X-RAY DIFFRACTION9chain 'B' and (resid 327 through 338 )B327 - 338
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 346 )B339 - 346
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 5 )C1 - 5
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 15 )C6 - 15
13X-RAY DIFFRACTION13chain 'C' and (resid 16 through 20 )C16 - 20
14X-RAY DIFFRACTION14chain 'F' and (resid 1 through 5 )F1 - 5
15X-RAY DIFFRACTION15chain 'F' and (resid 6 through 10 )F6 - 10
16X-RAY DIFFRACTION16chain 'F' and (resid 11 through 15 )F11 - 15
17X-RAY DIFFRACTION17chain 'F' and (resid 16 through 20 )F16 - 20

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