1NQ7

Characterization of ligands for the orphan nuclear receptor RORbeta

> Summary

Summary for 1NQ7

DescriptorNUCLEAR RECEPTOR ROR-BETA
Functional Keywordsligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription
Biological sourceRattus norvegicus (Norway rat)
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Cellular locationNucleus (Probable) P45446
Total number of polymer chains2
Total molecular weight29798.87
Authors
Stehlin-Gaon, C.,Willmann, D.,Sanglier, S.,Van Dorsselaer, A.,Renaud, J.-P.,Moras, D.,Schuele, R. (deposition date: 2003-01-21, release date: 2003-09-23, modification date: 2008-12-23)
Primary citation
Stehlin-Gaon, C.,Willmann, D.,Zeyer, D.,Sanglier, S.,Van Dorsselaer, A.,Renaud, J.-P.,Moras, D.,Schuele, R.
All-trans retinoic acid is a ligand for the orphan nuclear receptor RORbeta
Nat.Struct.Biol., 10:820-825, 2003
PubMed: 12958591
DOI: 10.1038/nsb979
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.5 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2221002.6%5.5%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1nq7
no rotation
Molmil generated image of 1nq7
rotated about x axis by 90°
Molmil generated image of 1nq7
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ANUCLEAR RECEPTOR ROR-BETApolymer24428167.81
UniProt (P45446)
Pfam (PF00104)
Rattus norvegicus (Norway rat)@PDBjNUCLEAR RECEPTOR RZR-BETA
BSTEROID RECEPTOR COACTIVATOR-1polymer101290.61
GenBank (AAB50242)
Pfam (PF08832)
UniProt (by SIFTS) (Q15788)
7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACIDnon-polymer340.51
waterwater18.0373

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight29458.4
Non-Polymers*Number of molecules1
Total molecular weight340.5
All*Total molecular weight29798.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.5 Å)

Cell axes52.82358.343105.668
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits19.87 - 1.50
the highest resolution shell value1.590 - 1.500
R-factor0.201
R-work0.20100
the highest resolution shell value0.222
R-free0.22000
the highest resolution shell value0.244
RMSD bond length0.006
RMSD bond angle1.100 (1.077*)

Data Collection Statistics

Resolution limits20.00 - 1.50
the highest resolution shell value -
Number of reflections52613 (53123*)
Rmerge_l_obs0.061*
the highest resolution shell value0.167*
Completeness99.2 (100.0*)
Redundancy8.8
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP (unknown*)8293unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*
Potier, N., (2003) Protein Sci., 12, 725.

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
B0005737cellular_componentcytoplasm
B0043005cellular_componentneuron projection
B0000790cellular_componentnuclear chromatin
B0005654cellular_componentnucleoplasm
B0050681molecular_functionandrogen receptor binding
B0003682molecular_functionchromatin binding
B0019899molecular_functionenzyme binding
B0004402molecular_functionhistone acetyltransferase activity
B0016922molecular_functionligand-dependent nuclear receptor binding
B0030374molecular_functionligand-dependent nuclear receptor transcription coactivator activity
B0035257molecular_functionnuclear hormone receptor binding
B0047485molecular_functionprotein N-terminus binding
B0001012molecular_functionRNA polymerase II regulatory region DNA binding
B0001105molecular_functionRNA polymerase II transcription coactivator activity
B0003713molecular_functiontranscription coactivator activity
B0030521biological_processandrogen receptor signaling pathway
B0015721biological_processbile acid and bile salt transport
B0044255biological_processcellular lipid metabolic process
B0032870biological_processcellular response to hormone stimulus
B1904017biological_processcellular response to Thyroglobulin triiodothyronine
B0021549biological_processcerebellum development
B0021987biological_processcerebral cortex development
B0044849biological_processestrous cycle
B0021766biological_processhippocampus development
B0043967biological_processhistone H4 acetylation
B0021854biological_processhypothalamus development
B0030522biological_processintracellular receptor signaling pathway
B0060713biological_processlabyrinthine layer morphogenesis
B0007595biological_processlactation
B0008584biological_processmale gonad development
B0060179biological_processmale mating behavior
B0043065biological_processpositive regulation of apoptotic process
B0045925biological_processpositive regulation of female receptivity
B0045666biological_processpositive regulation of neuron differentiation
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0000435biological_processpositive regulation of transcription from RNA polymerase II promoter by galactose
B0045893biological_processpositive regulation of transcription, DNA-templated
B2001038biological_processregulation of cellular response to drug
B0002155biological_processregulation of thyroid hormone mediated signaling pathway
B0032355biological_processresponse to estradiol
B0032570biological_processresponse to progesterone
B0032526biological_processresponse to retinoic acid
B0006351biological_processtranscription, DNA-templated
A0005634cellular_componentnucleus
A0008502molecular_functionmelatonin receptor activity
A0004879molecular_functionRNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
A0043565molecular_functionsequence-specific DNA binding
A0003707molecular_functionsteroid hormone receptor activity
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0008270molecular_functionzinc ion binding
A0035881biological_processamacrine cell differentiation
A0007420biological_processbrain development
A0071300biological_processcellular response to retinoic acid
A0007623biological_processcircadian rhythm
A0042462biological_processeye photoreceptor cell development
A0045668biological_processnegative regulation of osteoblast differentiation
A0045892biological_processnegative regulation of transcription, DNA-templated
A0045893biological_processpositive regulation of transcription, DNA-templated
A0042752biological_processregulation of circadian rhythm
A0009725biological_processresponse to hormone
A0060041biological_processretina development in camera-type eye
A0046549biological_processretinal cone cell development
A0046548biological_processretinal rod cell development
A0006351biological_processtranscription, DNA-templated
A0007601biological_processvisual perception
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC111BINDING SITE FOR RESIDUE ARL A 800
ChainResidue
ACYS20
AGLN21
ATYR22
ACYS55
ALEU93
AARG99
AMET100
ALEU112
APHE123
AHOH
AHOH

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
ARL_1nq7_A_800277-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID binding site
ChainResidueligand
ATHR226-TYR229ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
ACYS262ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AILE266ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AALA269ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
ATYR272ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
ALEU300ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AVAL303-LEU304ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AARG306-MET307ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AARG309-ALA310ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AVAL318-PHE320ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
APHE330ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
ALEU333ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
ALEU338-VAL339ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AALA342-PHE343ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AVAL419-CYS420ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID
AHIS423ARL: 7-(3,5-DITERT-BUTYLPHENYL)-3-METHYLOCTA-2,4,6-TRIENOIC ACID

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Nuclear receptor.
ChainResidueDetails
ANA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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