[English] 日本語
Yorodumi
- PDB-1exa: ENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF TH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1exa
TitleENANTIOMER DISCRIMINATION ILLUSTRATED BY CRYSTAL STRUCTURES OF THE HUMAN RETINOIC ACID RECEPTOR HRARGAMMA LIGAND BINDING DOMAIN: THE COMPLEX WITH THE ACTIVE R-ENANTIOMER BMS270394.
ComponentsRETINOIC ACID RECEPTOR GAMMA-2
KeywordsGENE REGULATION / enantiomer discrimination / retinoid ligand complexes / antiparallel alpha-helical sandwich fold / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


regulation of myeloid cell differentiation / Harderian gland development / trachea cartilage development / growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation ...regulation of myeloid cell differentiation / Harderian gland development / trachea cartilage development / growth plate cartilage chondrocyte growth / embryonic eye morphogenesis / embryonic camera-type eye development / glandular epithelial cell development / prostate gland epithelium morphogenesis / positive regulation of programmed cell death / negative regulation of chondrocyte differentiation / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / regulation of myelination / Signaling by Retinoic Acid / regulation of cell size / face development / canonical Wnt signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / retinoic acid receptor signaling pathway / negative regulation of stem cell proliferation / cellular response to retinoic acid / cellular response to leukemia inhibitory factor / stem cell proliferation / neural tube closure / multicellular organism growth / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / transcription regulator complex / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
: / : / Retinoic acid 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. ...: / : / Retinoic acid 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-394 / Retinoic acid receptor gamma / Retinoic acid receptor gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsKlaholz, B.P. / Mitschler, A. / Belema, M. / Zusi, C. / Moras, D. / Structural Proteomics in Europe (SPINE)
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Enantiomer discrimination illustrated by high-resolution crystal structures of the human nuclear receptor hRARgamma.
Authors: Klaholz, B.P. / Mitschler, A. / Belema, M. / Zusi, C. / Moras, D.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Conformational adaptation of agonists to the human nuclear receptor hRARgamma.
Authors: Klaholz, B.P. / Renaud, J.-P. / Mitschler, A. / Zusi, C. / Chambon, P. / Gronemeyer, H. / Moras, D.
#2: Journal: To be Published / Year: 2000
Title: Structural basis for isotype selectivity of the human retinoic acid nuclear receptor.
Authors: Klaholz, B.P. / Mitschler, A. / Moras, D.
History
DepositionMay 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: RETINOIC ACID RECEPTOR GAMMA-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8013
Polymers27,8901
Non-polymers9102
Water5,621312
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.672, 59.672, 155.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein RETINOIC ACID RECEPTOR GAMMA-2


Mass: 27890.498 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P22932, UniProt: P13631*PLUS
#2: Chemical ChemComp-394 / R-3-FLUORO-4-[2-HYDROXY-2-(5,5,8,8-TETRAMETHYL-5,6,7,8,-TETRAHYDRO-NAPHTALEN-2-YL)-ACETYLAMINO]-BENZOIC ACID / BMS270394


Mass: 399.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26FNO4
#3: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
Chemical formula: NaOAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.59→15 Å / Num. all: 37688 / Num. obs: 37688 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 27
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Num. unique all: 1738 / Rsym value: 0.308 / % possible all: 91.2
Reflection
*PLUS
Num. measured all: 131831
Reflection shell
*PLUS
% possible obs: 91.2 % / Rmerge(I) obs: 0.308

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LBD

4lbd


Resolution: 1.59→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1873 5 %random
Rwork0.209 ---
all-37646 --
obs-35773 97.3 %-
Refinement stepCycle: LAST / Resolution: 1.59→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 64 312 2317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.635
X-RAY DIFFRACTIONc_dihedral_angle_d1.078
X-RAY DIFFRACTIONc_improper_angle_d25.828
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg1.078
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg25.828

+
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