[English] 日本語
Yorodumi
- PDB-6eu9: Crystal structure of Platynereis dumerilii RAR ligand-binding dom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eu9
TitleCrystal structure of Platynereis dumerilii RAR ligand-binding domain in complex with all-trans retinoic acid
ComponentsRetinoic acid receptor
KeywordsTRANSCRIPTION / Retinoic acid / ancestral receptor / sensor
Function / homology
Function and homology information


cellular response to corticotropin-releasing hormone stimulus / nuclear glucocorticoid receptor binding / retinoic acid receptor signaling pathway / nuclear receptor activity / transcription regulator complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleus
Similarity search - Function
Retinoic acid receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RETINOIC ACID / Retinoic acid receptor
Similarity search - Component
Biological speciesPlatynereis dumerilii (Dumeril's clam worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.69 Å
AuthorsHandberg-Thorsager, M. / Gutierrez-Mazariegos, J. / Arold, S.T. / Nadendla, E.K. / Bertucci, P.Y. / Germain, P. / Tomancak, P. / Pierzchalski, K. / Jones, J.W. / Albalat, R. ...Handberg-Thorsager, M. / Gutierrez-Mazariegos, J. / Arold, S.T. / Nadendla, E.K. / Bertucci, P.Y. / Germain, P. / Tomancak, P. / Pierzchalski, K. / Jones, J.W. / Albalat, R. / Kane, M.A. / Bourguet, W. / Laudet, V. / Arendt, D. / Schubert, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INBS-05 France
CitationJournal: Sci Adv / Year: 2018
Title: The ancestral retinoic acid receptor was a low-affinity sensor triggering neuronal differentiation.
Authors: Handberg-Thorsager, M. / Gutierrez-Mazariegos, J. / Arold, S.T. / Kumar Nadendla, E. / Bertucci, P.Y. / Germain, P. / Tomancak, P. / Pierzchalski, K. / Jones, J.W. / Albalat, R. / Kane, M.A. ...Authors: Handberg-Thorsager, M. / Gutierrez-Mazariegos, J. / Arold, S.T. / Kumar Nadendla, E. / Bertucci, P.Y. / Germain, P. / Tomancak, P. / Pierzchalski, K. / Jones, J.W. / Albalat, R. / Kane, M.A. / Bourguet, W. / Laudet, V. / Arendt, D. / Schubert, M.
History
DepositionOct 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinoic acid receptor
B: Retinoic acid receptor
C: Retinoic acid receptor
D: Retinoic acid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4356
Polymers109,8344
Non-polymers6012
Water82946
1
C: Retinoic acid receptor

A: Retinoic acid receptor


Theoretical massNumber of molelcules
Total (without water)54,9172
Polymers54,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
2
B: Retinoic acid receptor
hetero molecules

D: Retinoic acid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5184
Polymers54,9172
Non-polymers6012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area4810 Å2
ΔGint-39 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.410, 68.150, 95.080
Angle α, β, γ (deg.)90.000, 100.750, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Retinoic acid receptor


Mass: 27458.439 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Platynereis dumerilii / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A384E144*PLUS
#2: Chemical ChemComp-REA / RETINOIC ACID


Mass: 300.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium acetate, 0.1 M HEPES pH 7.5, 20% PEG 3000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 32596 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rpim(I) all: 0.035 / Rrim(I) all: 0.064 / Rsym value: 0.053 / Net I/av σ(I): 6.7 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.69-2.783.50.5891.332250.3690.6970.58999.7
2.78-2.893.40.4571.730750.2890.5420.45799.4
2.89-3.013.30.3452.229770.2230.4120.34599.5
3.01-3.143.10.2243.428490.1510.2710.22499.2
3.14-3.293.40.1714.427310.1090.2030.17199
3.29-3.473.30.1076.925820.070.1290.10799
3.47-3.683.10.0738.724370.0490.0890.07398.7
3.68-3.9430.05112.422790.0350.0620.05197.9
3.94-4.253.20.03814.721440.0250.0460.03899.1
4.25-4.663.20.0351319590.0230.0420.03598.1
4.66-5.2130.02719.417840.0190.0330.02797.5
5.21-6.023.30.03216.615770.0210.0390.03299.2
6.02-7.3730.0317.713410.0210.0370.0397.1
7.37-10.423.20.02710.510430.0190.0330.02797.2
10.42-46.70530.02612.15930.0180.0320.02697.1

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MoRDaphasing
RefinementResolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / SU B: 40.416 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.23 / ESU R Free: 0.396
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 1633 5 %RANDOM
Rwork0.2551 ---
obs0.2573 30964 98.58 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.28 Å2 / Biso mean: 52.951 Å2 / Biso min: 15.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å2-2.29 Å2
2---2.2 Å20 Å2
3---0.84 Å2
Refinement stepCycle: final / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7069 0 44 46 7159
Biso mean--71.97 40.02 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197218
X-RAY DIFFRACTIONr_angle_refined_deg2.232.0059771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54224.773308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.517151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.4341545
X-RAY DIFFRACTIONr_chiral_restr0.1460.21170
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215278
LS refinement shellResolution: 2.69→2.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 126 -
Rwork0.378 2295 -
all-2421 -
obs--99.63 %

+
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