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- PDB-6eu9: Crystal structure of Platynereis dumerilii RAR ligand-binding dom... -

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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


retinoic acid receptor signaling pathway / nuclear receptor activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Retinoic acid


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


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 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

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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

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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 %

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