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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE ORPHAN NUCLEAR HORMONE RECEPTOR ROR(ALPHA)-LBD AND CHOLESTEROL
 
Authors :  J. A. Kallen, J. M. Schlaeppi, F. Bitsch, S. Geisse, M. Geiser, I. Delhon, B. Fournier
Date :  19 Nov 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A
Keywords :  Three-Layered Alpha Helical Sandwich, Receptor, Transcription Regulation, Nuclear Protein, Dna Binding, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Kallen, J. M. Schlaeppi, F. Bitsch, S. Geisse, M. Geiser, I. Delhon, B. Fournier
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 V. 10 1697 2002
PubMed-ID: 12467577  |  Reference-DOI: 10.1016/S0969-2126(02)00912-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR ROR-ALPHA
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: VIRUS
    Fragment: LIGAND BINDING DOMAIN, RESIDUES 304-556
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR RZR-ALPHA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CLR1Ligand/IonCHOLESTEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:320 , LYS A:326 , ILE A:327 , ALA A:330 , VAL A:364 , MET A:368 , TYR A:380 , LEU A:394 , HOH A:1005 , HOH A:1008 , HOH A:1020BINDING SITE FOR RESIDUE CLR A 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N83)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N83)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N83)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N83)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003356701ENSE00001323632chr15:61521518-61521252267RORA_HUMAN1-56560--
1.2ENST000003356702ENSE00001385043chr15:60970885-6097085630RORA_HUMAN56-66110--
1.8ENST000003356708ENSE00001651352chr15:60824050-6082396586RORA_HUMAN66-94290--
1.9ENST000003356709ENSE00001032968chr15:60806956-60806815142RORA_HUMAN95-142480--
1.10ENST0000033567010ENSE00000691384chr15:60803820-60803425396RORA_HUMAN142-2741331A:261-274 (gaps)54
1.11ENST0000033567011ENSE00001032962chr15:60797828-60797707122RORA_HUMAN274-314411A:274-31441
1.12ENST0000033567012ENSE00000391550chr15:60795866-60795734133RORA_HUMAN315-359451A:315-35945
1.13ENST0000033567013ENSE00000691379chr15:60795066-60794959108RORA_HUMAN359-395371A:359-39537
1.14ENST0000033567014ENSE00000885025chr15:60793268-60793158111RORA_HUMAN395-432381A:395-43238
1.15ENST0000033567015ENSE00000885024chr15:60792203-60792091113RORA_HUMAN432-469381A:432-46938
1.16bENST0000033567016bENSE00001141437chr15:60789818-607804839336RORA_HUMAN470-523541A:470-51142

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:251
 aligned with RORA_HUMAN | P35398 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:291
                                   230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510 
           RORA_HUMAN   221 FYLDIQPSPDQSGLDINGIKPEPICDYTPASGFFPYCSFTNGETSPTVSMAELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELF 511
               SCOP domains d1n83a                                _ A    :     Orphan nuclear receptor ROR-alpha                                                                                                                                                                                                                SCOP domains
               CATH domains 1n83A0                                0 A    :    261-511 Retinoid X Receptor                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------Hormone_recep-1n83A01 A:335-511                                                                                                                                                   Pfam domains
         Sec.struct. author hhhhhh--------------------------------hhh----h----hhhhhhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:261-274 (gaps) UniProt: 142-274     ----------------------------------------Exon 1.12  PDB: A:315-359 UniProt: 315-359   -----------------------------------Exon 1.14  PDB: A:395-432             -------------------------------------Exon 1.16b  PDB: A:470-511 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------Exon 1.11  PDB: A:274-314                --------------------------------------------Exon 1.13  PDB: A:359-395            ------------------------------------Exon 1.15  PDB: A:432-469             ------------------------------------------ Transcript 1 (2)
                 1n83 A 261 HHLEVL--------------------------------FQG----P----AELEHLAQNISKSHLETCQYLREELQQITWQTFLQEEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHREDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELF 511
                                 |   -         -         -       268|    |   -|      280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510 
                               266                              267 |  270  271                                                                                                                                                                                                                                                
                                                                  269
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Hormone_recep] (290)

(-) Gene Ontology  (53, 53)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RORA_HUMAN | P35398)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    GO:0001046    core promoter sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008142    oxysterol binding    Interacting selectively and non-covalently with oxysterol, an oxidized form of cholesterol.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0001223    transcription coactivator binding    Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0001222    transcription corepressor binding    Interacting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery.
    GO:0098531    transcription factor activity, direct ligand regulated sequence-specific DNA binding    A DNA binding transcription factor activity that is directly regulated by binding of a ligand to the protein with this activity. Examples include the lac and trp repressors in E.coli and many steroid hormone receptors.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0072539    T-helper 17 cell differentiation    The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 17 (Th17) cell. A Th17 cell is a CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive that produces IL-17.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0046068    cGMP metabolic process    The chemical reactions and pathways involving cyclic GMP, guanosine 3',5'-phosphate.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0071347    cellular response to interleukin-1    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0036315    cellular response to sterol    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sterol stimulus.
    GO:0071356    cellular response to tumor necrosis factor    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
    GO:0021702    cerebellar Purkinje cell differentiation    The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar Purkinje cell. Differentiation includes the processes involved in commitment of a neuroblast to a Purkinje cell fate. A Purkinje cell is an inhibitory GABAergic neuron found in the cerebellar cortex that projects to the deep cerebellar nuclei and brain stem.
    GO:0021930    cerebellar granule cell precursor proliferation    The multiplication or reproduction of neuroblasts that will give rise to granule cells. A granule cell is a glutamatergic interneuron found in the cerebellar cortex.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0042692    muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a muscle cell.
    GO:0043124    negative regulation of I-kappaB kinase/NF-kappaB signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling.
    GO:0045599    negative regulation of fat cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0006809    nitric oxide biosynthetic process    The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water.
    GO:0042753    positive regulation of circadian rhythm    Any process that activates or increases the frequency, rate or extent of a circadian rhythm behavior.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0010575    positive regulation of vascular endothelial growth factor production    Any process that increases or activates the frequency, rate, or extent of production of vascular endothelial growth factor.
    GO:2000188    regulation of cholesterol homeostasis    Any process that modulates the frequency, rate or extent of cholesterol homeostasis.
    GO:0042752    regulation of circadian rhythm    Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0010906    regulation of glucose metabolic process    Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0043030    regulation of macrophage activation    Any process that modulates the frequency or rate of macrophage activation.
    GO:0008589    regulation of smoothened signaling pathway    Any process that modulates the frequency, rate or extent of smoothened signaling.
    GO:0019218    regulation of steroid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids.
    GO:0060850    regulation of transcription involved in cell fate commitment    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter that contributes to the commitment of a cell to a specific fate.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0070328    triglyceride homeostasis    Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  1n83
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RORA_HUMAN | P35398: 1s0x 4s15

(-) Related Entries Specified in the PDB File

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