[English] 日本語
Yorodumi
- PDB-5yd6: Crystal structure of PG-bound Nurr1-LBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yd6
TitleCrystal structure of PG-bound Nurr1-LBD
ComponentsNuclear receptor subfamily 4 group A member 2
KeywordsTRANSCRIPTION / NURR1 / LBD / PROSTAGLANDIN / MICHAEL ADDITION
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
Chem-8SU / Nuclear receptor subfamily 4 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsSreekanth, R. / Yoon, H.S.
CitationJournal: To Be Published
Title: Structure of Nurr1 bound to cyclopentenone prostaglandin A2 and its mechanism of action in ameliorating dopaminergic neurodegeneration in Drosophila
Authors: Rajan, S. / Toh, H.T. / Lim, K.H. / Yoon, H.S.
History
DepositionSep 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,69110
Polymers122,3054
Non-polymers1,3866
Water5,891327
1
A: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9353
Polymers30,5761
Non-polymers3592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11320 Å2
MethodPISA
2
B: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9353
Polymers30,5761
Non-polymers3592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11520 Å2
MethodPISA
3
C: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9112
Polymers30,5761
Non-polymers3341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-3 kcal/mol
Surface area11460 Å2
MethodPISA
4
D: Nuclear receptor subfamily 4 group A member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9112
Polymers30,5761
Non-polymers3341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50 Å2
ΔGint-3 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.950, 94.080, 135.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: 30576.256 Da / Num. of mol.: 4 / Fragment: UNP residues 328-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2, NOT, NURR1, TINUR / Plasmid: PET-SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: P43354
#2: Chemical
ChemComp-8SU / (~{Z})-7-[(1~{R},5~{S})-2-oxidanylidene-5-[(~{E},3~{S})-3-oxidanyloct-1-enyl]cyclopent-3-en-1-yl]hept-5-enoic acid / PROSTAGLANDIN A2 (PGA2)


Mass: 334.450 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H30O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, MES PH 5.5 AND MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→94.08 Å / Num. obs: 46996 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 12.8
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 6778 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVL

1ovl


Resolution: 2.34→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 19.847 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.265
RfactorNum. reflection% reflectionSelection details
Rfree0.26863 2343 5 %RANDOM
Rwork0.22507 ---
obs0.22722 44489 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.042 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å20 Å2
2--3.04 Å20 Å2
3----2.47 Å2
Refinement stepCycle: 1 / Resolution: 2.34→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7199 0 98 327 7624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.98710067
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2155889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02224.353340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.577151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4911544
X-RAY DIFFRACTIONr_chiral_restr0.0980.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215552
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7512.9063592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2934.3534469
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1563.0713856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.97241.17311281
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 182 -
Rwork0.328 3200 -
obs--99.82 %
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)
13.81870.73481.11772.3574-0.95444.06570.0535-0.16780.320.0973-0.07620.1316-0.1025-0.02380.02280.0067-0.00550.0120.1006-0.05320.0582-8.8948-19.78037.8552
23.59120.3691.23192.5368-1.43763.8879-0.2212-0.16810.33180.02440.07220.03730.0217-0.12090.1490.04510.0574-0.04240.1498-0.07090.0569-17.693227.21457.5683
32.85990.69561.49673.09031.62095.2712-0.07210.30450.2833-0.1724-0.0619-0.5058-0.30310.41370.13390.04990.00090.0370.22480.13080.1875-19.0339-15.5639-23.7748
43.1091.06771.84042.76461.55125.59640.00230.26340.15980.0208-0.0336-0.51030.25450.27710.03130.03580.0016-0.0050.19010.08990.1604-27.874831.1158-24.1113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A362 - 598
2X-RAY DIFFRACTION2B362 - 598
3X-RAY DIFFRACTION3C360 - 598
4X-RAY DIFFRACTION4D360 - 598

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more