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- PDB-6l6l: Structural basis of NR4A2 homodimers binding to selective Nur-res... -

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Basic information

Entry
Database: PDB / ID: 6l6l
TitleStructural basis of NR4A2 homodimers binding to selective Nur-responsive elements
Components
  • DNA (5'-D(*AP*AP*AP*GP*GP*TP*CP*AP*AP*AP*CP*TP*GP*TP*GP*AP*CP*CP*TP*AP*T)-3')
  • DNA (5'-D(P*TP*AP*TP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*TP*TP*GP*AP*CP*CP*TP*T)-3')
  • Nuclear receptor related 1
KeywordsDNA BINDING PROTEIN / NR4A2/Nurr1 / nuclear receptors
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: 2.781 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(*AP*AP*AP*GP*GP*TP*CP*AP*AP*AP*CP*TP*GP*TP*GP*AP*CP*CP*TP*AP*T)-3')
D: DNA (5'-D(P*TP*AP*TP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*TP*TP*GP*AP*CP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5388
Polymers32,2764
Non-polymers2624
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-30 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.405, 64.315, 60.776
Angle α, β, γ (deg.)90.000, 96.840, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 263 through 340 or (resid 341...
21(chain B and resid 263 through 345)

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSGLYGLY(chain A and (resid 263 through 340 or (resid 341...AA263 - 3402 - 79
12ARGARGARGARG(chain A and (resid 263 through 340 or (resid 341...AA34180
13LEULEUPROPRO(chain A and (resid 263 through 340 or (resid 341...AA262 - 3461 - 85
14LEULEUPROPRO(chain A and (resid 263 through 340 or (resid 341...AA262 - 3461 - 85
15LEULEUPROPRO(chain A and (resid 263 through 340 or (resid 341...AA262 - 3461 - 85
16LEULEUPROPRO(chain A and (resid 263 through 340 or (resid 341...AA262 - 3461 - 85
21CYSCYSLEULEU(chain B and resid 263 through 345)BB263 - 3452 - 84

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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(*AP*AP*AP*GP*GP*TP*CP*AP*AP*AP*CP*TP*GP*TP*GP*AP*CP*CP*TP*AP*T)-3')


Mass: 6455.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*TP*AP*TP*AP*GP*GP*TP*CP*AP*CP*AP*GP*TP*TP*TP*GP*AP*CP*CP*TP*T)-3')


Mass: 6428.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 50 mM Na acetate (pH 4.7), 200 mM NaCl, 10 mM MgCl2, 5 mM Li2SO4, 5 mM DTT, and 15-19% 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
ReflectionResolution: 2.781→35.23 Å / Num. obs: 8163 / % possible obs: 98.67 % / Redundancy: 3.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1162 / Rrim(I) all: 0.1384 / Net I/σ(I): 6.69
Reflection shellResolution: 2.781→2.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3742 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 737 / CC1/2: 0.885 / % possible all: 89.99

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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: 2.781→35.226 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.97
RfactorNum. reflection% reflection
Rfree0.252 809 9.98 %
Rwork0.2163 --
obs0.2199 8109 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.04 Å2 / Biso mean: 41.6697 Å2 / Biso min: 3.65 Å2
Refinement stepCycle: final / Resolution: 2.781→35.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1319 858 4 24 2205
Biso mean--31.05 20.53 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042298
X-RAY DIFFRACTIONf_angle_d0.7513258
X-RAY DIFFRACTIONf_chiral_restr0.036355
X-RAY DIFFRACTIONf_plane_restr0.003275
X-RAY DIFFRACTIONf_dihedral_angle_d19.6791248
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A776X-RAY DIFFRACTION8.789TORSIONAL
12B776X-RAY DIFFRACTION8.789TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.781-2.95510.37261270.304115894
2.9551-3.18320.33751370.3021121899
3.1832-3.50320.29331310.2477119597
3.5032-4.00960.23431360.20671217100
4.0096-5.04930.22851380.18921250100
5.0493-35.2260.18811400.1643126299
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)
10.595-0.16730.1430.58860.18831.33610.28920.1846-0.2180.04070.01740.11670.3731-0.434-0.07130.39650.0197-0.03120.41920.00120.3347-18.9241-21.4514-19.901
24.1997-1.05730.30171.0263-0.82880.78690.12670.67210.6578-0.45930.07440.2642-0.11670.00110.05970.5623-0.1169-0.13050.3376-0.09270.3466-7.3581-13.2077-11.5231
30.5797-0.34640.32010.9265-0.28851.6156-0.0805-0.1501-0.9314-0.1350.3077-0.0541-0.003-0.2105-0.09690.39920.0041-0.10630.22550.00390.3683-8.4224-28.2917-10.1831
41.16280.26351.93120.05780.41523.24630.3190.51280.1670.730.1713-0.62520.48121.2694-0.08530.41630.0212-0.13880.29540.01180.4796-8.4666-21.6924-17.1037
54.0415-1.9832-0.33572.777-0.99290.71780.21120.08251.4772-0.4586-0.107-0.9127-0.82591.07550.04270.7717-0.0244-0.06210.3994-0.00560.461-16.6166-9.5162-24.671
61.84550.01720.50640.25381.14825.1147-0.2088-0.64030.5957-0.5330.28910.60430.0449-0.6248-0.02620.68820.0678-0.22460.52120.05170.9174-27.193-7.5575-26.6689
71.3001-0.21961.31281.9426-0.90881.5381-0.21320.10550.7435-0.0199-0.1615-0.5446-0.02790.0937-0.04180.50140.113-0.09430.39-0.06060.5144-3.1405-1.45115.0908
80.69750.1431-0.71670.18730.01120.9875-0.2184-0.02870.39050.9326-0.1844-0.3329-0.3920.0204-0.18770.5838-0.0166-0.18630.3343-0.06060.43451.9021-8.0216.7738
91.20840.27320.99112.60771.24361.4385-0.05950.0652-0.12341.2155-0.0950.22990.6594-0.1375-0.10420.31630.0305-0.10520.38270.00780.3825-3.2208-14.90519.4491
101.26751.6903-0.81763.0573-2.98038.3081-0.1321-0.1894-0.43230.0283-0.2117-0.89280.41410.0069-0.07130.4848-0.0229-0.08720.46090.03510.2921-1.5447-15.4736-2.0423
111.2391-0.1729-1.15860.01740.15241.08590.1992-0.19070.6535-0.06280.21880.3014-0.44090.66230.42130.8229-0.314-0.0836-0.14670.37490.5256-2.5703-3.3699-7.8161
121.9495-1.3650.29231.92411.31015.02680.61650.36230.4704-0.3041-0.2808-1.0047-0.85280.3242-0.11170.3584-0.06830.07520.39330.18150.7332-4.27760.98661.3115
131.0114-0.2266-1.75772.36312.86782.00080.1998-0.28760.1879-0.49480.24040.1021-0.6951-1.28231.0360.25360.0583-0.22120.4568-0.03090.6259-9.9577-1.82794.365
140.2986-0.30150.59120.4056-0.83481.7582-0.6450.0970.85120.3099-0.4484-0.3269-0.94570.677-0.20780.3378-0.0495-0.07530.3412-0.01140.40730.8279-6.81682.9872
158.01223.73342.00471.748-5.44661.9966-1.19960.1156-1.6271-0.4055-1.2306-0.3991.06091.0832-1.22670.2308-0.096-0.18880.38540.01270.4797.2427-13.80899.944
161.75170.55791.57810.47070.63223.16590.16430.8787-0.12460.98320.8869-0.035-0.07830.53580.00910.78350.1572-0.04280.4978-0.01040.64433.7785-24.075317.5592
17-0.02770.33670.29350.71720.15611.36430.1117-0.0918-0.2792-0.09540.05120.10730.0934-0.7537-0.05150.43960.0427-0.13420.6764-0.02080.4529-23.4788-16.3732-7.4603
181.6895-1.17650.77581.5847-1.42261.3412-0.3447-0.3474-0.58371.37620.0509-0.2908-0.65940.3401-0.14240.6156-0.0586-0.14140.55210.03240.4894-7.8538-17.128524.4926
193.96841.37340.90342.2998-1.642.25390.3126-0.96750.5760.7346-0.2514-0.1378-0.3847-1.352-0.02070.7897-0.0042-0.23880.5759-0.08760.51780.6884-14.384724.1878
201.1362-0.3867-0.36310.321-0.00141.33620.0819-0.45010.0290.29490.21410.13780.1648-1.0002-0.04580.529-0.0947-0.13320.5610.06260.4518-22.7273-17.4975-1.1829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 262 through 293 )A262 - 293
2X-RAY DIFFRACTION2chain 'A' and (resid 294 through 298 )A294 - 298
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 315 )A299 - 315
4X-RAY DIFFRACTION4chain 'A' and (resid 316 through 326 )A316 - 326
5X-RAY DIFFRACTION5chain 'A' and (resid 327 through 338 )A327 - 338
6X-RAY DIFFRACTION6chain 'A' and (resid 339 through 346 )A339 - 346
7X-RAY DIFFRACTION7chain 'B' and (resid 262 through 271 )B262 - 271
8X-RAY DIFFRACTION8chain 'B' and (resid 272 through 280 )B272 - 280
9X-RAY DIFFRACTION9chain 'B' and (resid 281 through 293 )B281 - 293
10X-RAY DIFFRACTION10chain 'B' and (resid 294 through 298 )B294 - 298
11X-RAY DIFFRACTION11chain 'B' and (resid 299 through 303 )B299 - 303
12X-RAY DIFFRACTION12chain 'B' and (resid 304 through 308 )B304 - 308
13X-RAY DIFFRACTION13chain 'B' and (resid 309 through 315 )B309 - 315
14X-RAY DIFFRACTION14chain 'B' and (resid 316 through 326 )B316 - 326
15X-RAY DIFFRACTION15chain 'B' and (resid 327 through 332 )B327 - 332
16X-RAY DIFFRACTION16chain 'B' and (resid 333 through 345 )B333 - 345
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 15 )C1 - 15
18X-RAY DIFFRACTION18chain 'C' and (resid 16 through 21 )C16 - 21
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 5 )D1 - 5
20X-RAY DIFFRACTION20chain 'D' and (resid 6 through 21 )D6 - 21

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