1N83

Crystal Structure of the complex between the Orphan Nuclear Hormone Receptor ROR(alpha)-LBD and Cholesterol

> Summary

Summary for 1N83

DescriptorNuclear receptor ROR-alpha
Functional Keywordsthree-layered alpha helical sandwich, receptor, transcription regulation, nuclear protein, dna binding, lipid binding protein
Biological sourceHomo sapiens (human)
Cellular locationNucleus P35398
Total number of polymer chains1
Total molecular weight31901.19
Authors
Kallen, J.A.,Schlaeppi, J.M.,Bitsch, F.,Geisse, S.,Geiser, M.,Delhon, I.,Fournier, B. (deposition date: 2002-11-19, release date: 2002-12-11, modification date: 2009-02-24)
Primary citation
Kallen, J.A.,Schlaeppi, J.M.,Bitsch, F.,Geisse, S.,Geiser, M.,Delhon, I.,Fournier, B.
X-ray Structure of hROR(alpha) LBD at 1.63A: Structural and Functional data that Cholesterol or a Cholesterol derivative is the natural ligand of ROR(alpha)
Structure, 10:1697-1702, 2002
PubMed: 12467577
DOI: 10.1016/S0969-2126(02)00912-7
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.63 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.228900.4%6.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1n83
no rotation
Molmil generated image of 1n83
rotated about x axis by 90°
Molmil generated image of 1n83
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ANuclear receptor ROR-alphapolymer27031514.51
UniProt (P35398)
Pfam (PF00104)
Homo sapiens (human)@PDBjnuclear receptor RZR-alpha
CHOLESTEROLnon-polymer386.71
waterwater18.0419

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight31514.5
Non-Polymers*Number of molecules1
Total molecular weight386.7
All*Total molecular weight31901.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.63 Å)
Cell axes54.80049.70060.500
Cell angles90.0098.4090.00
SpacegroupP 1 21 1
Resolution limits15.00 - 1.63
the highest resolution shell value1.672 - 1.630
R-factor0.2018
R-work0.20067 (0.19900*)
the highest resolution shell value0.260
R-free0.22277 (0.23000*)
the highest resolution shell value0.297
RMSD bond length0.009
RMSD bond angle1.135 (1.110*)

Data Collection Statistics

Resolution limits15.00 - 1.63
the highest resolution shell value -
Number of reflections38783
Number of measurements141730*
Rmerge_l_obs0.040*
Completeness95.4
Redundancy3.65
the highest resolution shell value2.5
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5 (8.4*)293 (20*)*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11reservoirTris-HCl100 (mM)pH8.4
21reservoirPEG600019 (%)
31reservoir0.2 (M)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0001046molecular_functioncore promoter sequence-specific DNA binding
A0003677molecular_functionDNA binding
A0008142molecular_functionoxysterol binding
A0000977molecular_functionRNA polymerase II regulatory region sequence-specific DNA binding
A0004879molecular_functionRNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding
A0043565molecular_functionsequence-specific DNA binding
A0003707molecular_functionsteroid hormone receptor activity
A0001223molecular_functiontranscription coactivator binding
A0001222molecular_functiontranscription corepressor binding
A0098531molecular_functiontranscription factor activity, direct ligand regulated sequence-specific DNA binding
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0008134molecular_functiontranscription factor binding
A0008270molecular_functionzinc ion binding
A0001525biological_processangiogenesis
A0071456biological_processcellular response to hypoxia
A0071347biological_processcellular response to interleukin-1
A0036315biological_processcellular response to sterol
A0071356biological_processcellular response to tumor necrosis factor
A0021930biological_processcerebellar granule cell precursor proliferation
A0021702biological_processcerebellar Purkinje cell differentiation
A0046068biological_processcGMP metabolic process
A0032922biological_processcircadian regulation of gene expression
A0007623biological_processcircadian rhythm
A0010467biological_processgene expression
A0030522biological_processintracellular receptor signaling pathway
A0042692biological_processmuscle cell differentiation
A0045599biological_processnegative regulation of fat cell differentiation
A0043124biological_processnegative regulation of I-kappaB kinase/NF-kappaB signaling
A0050728biological_processnegative regulation of inflammatory response
A0006809biological_processnitric oxide biosynthetic process
A0042753biological_processpositive regulation of circadian rhythm
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0045893biological_processpositive regulation of transcription, DNA-templated
A0010575biological_processpositive regulation of vascular endothelial growth factor production
A2000188biological_processregulation of cholesterol homeostasis
A0010906biological_processregulation of glucose metabolic process
A0043030biological_processregulation of macrophage activation
A0008589biological_processregulation of smoothened signaling pathway
A0019218biological_processregulation of steroid metabolic process
A0060850biological_processregulation of transcription involved in cell fate commitment
A0006355biological_processregulation of transcription, DNA-templated
A0072539biological_processT-helper 17 cell differentiation
A0006367biological_processtranscription initiation from RNA polymerase II promoter
A0070328biological_processtriglyceride homeostasis
A0006805biological_processxenobiotic metabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC111BINDING SITE FOR RESIDUE CLR A 1000
ChainResidue
ATRP67
ALYS73
AILE74
AALA77
AVAL111
AMET115
ATYR127
ALEU141
AHOH
AHOH
AHOH

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

site_idNumber of ResiduesDetails
CLR_1n83_A_100023CHOLESTEROL binding site
ChainResidueligand
ATRP320CLR: CHOLESTEROL
ACYS323-ALA324CLR: CHOLESTEROL
ALYS326-ILE327CLR: CHOLESTEROL
AALA330CLR: CHOLESTEROL
AVAL364-PHE365CLR: CHOLESTEROL
AARG367-MET368CLR: CHOLESTEROL
AARG370-ALA371CLR: CHOLESTEROL
AVAL379-PHE381CLR: CHOLESTEROL
APHE391CLR: CHOLESTEROL
ALEU394CLR: CHOLESTEROL
ACYS396CLR: CHOLESTEROL
APHE399-ILE400CLR: CHOLESTEROL
AVAL403CLR: CHOLESTEROL
AHIS484CLR: CHOLESTEROL
ATYR507CLR: CHOLESTEROL

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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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