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- PDB-7wnh: Crystal structure of Nurr1 binding to NBRE -

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Basic information

Entry
Database: PDB / ID: 7wnh
TitleCrystal structure of Nurr1 binding to NBRE
Components
  • DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
  • Nuclear receptor subfamily 4 group A member 2
KeywordsTRANSCRIPTION / Nurr1 / NBRE / DBD / LBD
Function / homology
Function and homology information


general adaptation syndrome / habenula development / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / nuclear glucocorticoid receptor binding / regulation of dopamine metabolic process / regulation of respiratory gaseous exchange / midbrain dopaminergic neuron differentiation / dopaminergic neuron differentiation / neuron maturation ...general adaptation syndrome / habenula development / cellular response to corticotropin-releasing hormone stimulus / central nervous system projection neuron axonogenesis / nuclear glucocorticoid receptor binding / regulation of dopamine metabolic process / regulation of respiratory gaseous exchange / midbrain dopaminergic neuron differentiation / dopaminergic neuron differentiation / neuron maturation / central nervous system neuron differentiation / dopamine biosynthetic process / 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 / SUMOylation of intracellular receptors / beta-catenin binding / Nuclear Receptor transcription pathway / nuclear receptor activity / neuron migration / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / transcription regulator complex / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / 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 / 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, NURR 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
DNA / DNA (> 10) / Nuclear receptor subfamily 4 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZhao, M. / Xu, T. / Wang, N. / Guo, Y. / Liu, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Integrative analysis reveals structural basis for transcription activation of Nurr1 and Nurr1-RXR alpha heterodimer.
Authors: Zhao, M. / Wang, N. / Guo, Y. / Li, J. / Yin, Y. / Dong, Y. / Zhu, J. / Peng, C. / Xu, T. / Liu, J.
History
DepositionJan 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Mar 15, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 subfamily 4 group A member 2
B: Nuclear receptor subfamily 4 group A member 2
C: Nuclear receptor subfamily 4 group A member 2
D: Nuclear receptor subfamily 4 group A member 2
E: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
F: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
H: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
I: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
K: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
L: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
N: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
O: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,13220
Polymers197,60812
Non-polymers5238
Water50428
1
A: Nuclear receptor subfamily 4 group A member 2
E: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
F: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5335
Polymers49,4023
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-14 kcal/mol
Surface area20540 Å2
MethodPISA
2
B: Nuclear receptor subfamily 4 group A member 2
K: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
L: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5335
Polymers49,4023
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-16 kcal/mol
Surface area21010 Å2
MethodPISA
3
C: Nuclear receptor subfamily 4 group A member 2
H: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
I: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5335
Polymers49,4023
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-15 kcal/mol
Surface area21460 Å2
MethodPISA
4
D: Nuclear receptor subfamily 4 group A member 2
N: DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')
O: DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5335
Polymers49,4023
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-12 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.002, 124.002, 119.518
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27I
18E
28L
19E
29O
110F
210H
111F
211K
112F
212N
113H
213K
114H
214N
115I
215L
116I
216O
117K
217N
118L
218O

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUPHEPHEAA262 - 59214 - 344
21LEULEUPHEPHEBB262 - 59214 - 344
12LEULEUPROPROAA262 - 59714 - 349
22LEULEUPROPROCC262 - 59714 - 349
13CYSCYSLEULEUAA263 - 59615 - 348
23CYSCYSLEULEUDD263 - 59615 - 348
14LEULEUPHEPHEBB262 - 59214 - 344
24LEULEUPHEPHECC262 - 59214 - 344
15CYSCYSLEULEUBB263 - 59115 - 343
25CYSCYSLEULEUDD263 - 59115 - 343
16CYSCYSLEULEUCC263 - 59615 - 348
26CYSCYSLEULEUDD263 - 59615 - 348
17DCDCDGDGEE261 - 2761 - 16
27DCDCDGDGIH261 - 2761 - 16
18DCDCDGDGEE261 - 2761 - 16
28DCDCDGDGLJ261 - 2761 - 16
19DCDCDGDGEE261 - 2761 - 16
29DCDCDGDGOL261 - 2761 - 16
110DCDCDGDGFF261 - 2761 - 16
210DCDCDGDGHG261 - 2761 - 16
111DCDCDGDGFF261 - 2761 - 16
211DCDCDGDGKI261 - 2761 - 16
112DCDCDGDGFF261 - 2761 - 16
212DCDCDGDGNK261 - 2761 - 16
113DCDCDGDGHG261 - 2761 - 16
213DCDCDGDGKI261 - 2761 - 16
114DCDCDGDGHG261 - 2761 - 16
214DCDCDGDGNK261 - 2761 - 16
115DCDCDGDGIH261 - 2761 - 16
215DCDCDGDGLJ261 - 2761 - 16
116DCDCDGDGIH261 - 2761 - 16
216DCDCDGDGOL261 - 2761 - 16
117DCDCDGDGKI261 - 2761 - 16
217DCDCDGDGNK261 - 2761 - 16
118DCDCDGDGLJ261 - 2761 - 16
218DCDCDGDGOL261 - 2761 - 16

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
Nuclear receptor subfamily 4 group A member 2 / Immediate-early response protein NOT / Orphan nuclear receptor NURR1 / Transcriptionally-inducible ...Immediate-early response protein NOT / Orphan nuclear receptor NURR1 / Transcriptionally-inducible nuclear receptor


Mass: 39604.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43354
#2: DNA chain
DNA (5'-D(*CP*GP*CP*AP*TP*GP*AP*CP*CP*TP*TP*TP*TP*CP*GP*G)-3')


Mass: 4865.152 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain
DNA (5'-D(*CP*CP*GP*AP*AP*AP*AP*GP*GP*TP*CP*AP*TP*GP*CP*G)-3')


Mass: 4932.218 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.68 Å3/Da / Density % sol: 54.18 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5
Details: 0.1M sodium malonate, pH5.0, 20% PEG3350,1.44% myo-lnositol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 3.1→119.52 Å / Num. obs: 37212 / % possible obs: 99.7 % / Redundancy: 9.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.056 / Rrim(I) all: 0.172 / Net I/σ(I): 7.9 / Num. measured all: 356012 / Scaling rejects: 4865
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.249.71.1024422645720.6420.3791.1681.899.9
10.74-119.527.90.0769718840.9980.0250.07516.398.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CIT,1OVL

1cit

1ovl


Resolution: 3.1→107.39 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.902 / SU B: 27.949 / SU ML: 0.465 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 1762 4.7 %RANDOM
Rwork0.2233 ---
obs0.2254 35419 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 246.73 Å2 / Biso mean: 84.256 Å2 / Biso min: 15.38 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0.88 Å2-0 Å2
2---1.76 Å2-0 Å2
3---5.72 Å2
Refinement stepCycle: final / Resolution: 3.1→107.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9908 2600 8 28 12544
Biso mean--122.11 50.98 -
Num. residues----1379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01212999
X-RAY DIFFRACTIONr_bond_other_d0.0010.01811066
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.52418073
X-RAY DIFFRACTIONr_angle_other_deg1.2231.76825707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49751237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89821.268560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.625151824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8261590
X-RAY DIFFRACTIONr_chiral_restr0.0650.21661
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022839
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89260.09
12B89260.09
21A92250.07
22C92250.07
31A89210.1
32D89210.1
41B90100.09
42C90100.09
51B92800.07
52D92800.07
61C90610.09
62D90610.09
71E13660.03
72I13660.03
81E13690.02
82L13690.02
91E13590.08
92O13590.08
101F14310.02
102H14310.02
111F14330.03
112K14330.03
121F14350.02
122N14350.02
131H14260.03
132K14260.03
141H14300.02
142N14300.02
151I13690.03
152L13690.03
161I13590.08
162O13590.08
171K14310.03
172N14310.03
181L13590.08
182O13590.08
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 128 -
Rwork0.337 2639 -
all-2767 -
obs--99.89 %

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