[English] 日本語
Yorodumi
- PDB-1ovl: Crystal Structure of Nurr1 LBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ovl
TitleCrystal Structure of Nurr1 LBD
Components(Orphan nuclear receptor NURR1 (MSE ...) x 2
KeywordsTRANSCRIPTION / Nuur1 / 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
BROMIDE ION / IODIDE ION / : / Nuclear receptor subfamily 4 group A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsWang, Z. / Liu, J. / Walker, N.
CitationJournal: Nature / Year: 2003
Title: Structure and Function of Nurr1 identifies a Class of Ligand-Independent Nuclear Receptors
Authors: Wang, Z. / Benoit, G. / Liu, J. / Prasad, S. / Aarnisalo, P. / Liu, X. / Xu, H. / Walker, N. / Perlmann, T.
History
DepositionMar 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Orphan nuclear receptor NURR1 (MSE 414, 496, 511)
B: Orphan nuclear receptor NURR1 (MSE 496, 511)
C: Orphan nuclear receptor NURR1 (MSE 496, 511)
D: Orphan nuclear receptor NURR1 (MSE 414, 496, 511)
E: Orphan nuclear receptor NURR1 (MSE 496, 511)
F: Orphan nuclear receptor NURR1 (MSE 496, 511)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,16634
Polymers184,2086
Non-polymers1,95828
Water10,124562
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.383, 80.383, 227.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

-
Orphan nuclear receptor NURR1 (MSE ... , 2 types, 6 molecules ADBCEF

#1: Protein Orphan nuclear receptor NURR1 (MSE 414, 496, 511) / Immediate-early response protein NOT / Transcriptionally inducible nuclear receptor


Mass: 30670.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 OR NURR1 OR TINUR OR NOT / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P43354
#2: Protein
Orphan nuclear receptor NURR1 (MSE 496, 511) / Immediate-early response protein NOT / Transcriptionally inducible nuclear receptor


Mass: 30716.936 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A2 OR NURR1 OR TINUR OR NOT / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: P43354

-
Non-polymers , 4 types, 590 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: PEG3350,KBr, Hepes, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-7 mg/mlprotein1drop
220 mMTris-HCl1droppH7.9
3100 mM1dropNaCl
42 mMEDTA1drop
55 mMdithiothreitol1drop
618 %(w/v)PEG33501reservoir
70.1 MHEPES1reservoirpH6.5
80.2 M1reservoirKBr

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2001
RadiationMonochromator: Double cyrstal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→34.7 Å / Num. all: 287222 / Num. obs: 82388 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.072 / Net I/σ(I): 6.2
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 2.4 / % possible all: 91.7
Reflection
*PLUS
Num. measured all: 287222 / Rmerge(I) obs: 0.072

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNXrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4117 -Radom
Rwork0.217 ---
all0.231 83435 --
obs0.231 82321 98.7 %-
Refinement stepCycle: LAST / Resolution: 2.2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11113 0 28 562 11703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_bond_d0.006
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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