1S0X,1N4H,1N83


Conserved Protein Domain Family
NR_LBD_ROR_like

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cd06939: NR_LBD_ROR_like 
Click on image for an interactive view with Cn3D
The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily
The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Statistics
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PSSM-Id: 132737
View PSSM: cd06939
Aligned: 12 rows
Threshold Bit Score: 367.076
Threshold Setting Gi: 74920801
Created: 19-Nov-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand bindingcoactivator
Conserved site includes 21 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:

Feature 1                      ###                   #  ## ##  #                              
1S0X_A     18 AELEHLAQNISKSHLETCQY.[16].EIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGS 107 human
1N4H_A     10 SEIDRIAQNIIKSHLETCQY.[16].EIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGC 99  Norway rat
1N83_A     18 AELEHLAQNISKSHLETCQY.[16].EIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGS 107 human
NP_990424 210 TEIDRIAQNIIKSHLETCQY.[16].EIKVYQSKTREALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGC 299 chicken
Q7ZU39    222 DDLEHLSENICKSHLETCQY.[16].NLEAYQKKSQEDMWQLCAVKVTEAVQYVVEFAKRIDGFMELCQNDQIVLLKAGS 311 zebrafish
CAG11892  264 CLLDELCASIVRAHRETSQW.[16].EIQAYQSKSVDEMWQHCAIRLTDAVQYVVEFAKHIPGFRMLTQNDQIALLKTGS 353 spotted green pufferfish
Q3ZBY9    280 TEIEHLVQNVCKSYRDTCQL.[16].EVAGYQRKSMWEMWGRCAHRLTEAIQYVVEFAKRLPGFMELCQNDQIVLLKAGA 369 cattle
Q4H2V2    380 NISENLVSNICEAYYKTCQY.[16].GTLQFQNMAPDQLWGLCAEKITEAIQHVVEFAKHSNAFMSFDQHDQIILLKTGC 469 Ciona intestinalis
Q5XG07    155 VELDLLMQNVVCAHRETCKF.[16].EIQSFQQKTMDEMWERCVCHITDAIQYIVEFAKRLNGFMELNPNDQIVLLKAGA 244 African clawed frog
Q7PWD9    192 DINDVLIKTLAEAHANTNHK.[15].RLLYYKNMTQEELWLDCAEKLTAMIQQIIEFAKLIPGFMRLSQDDQILLLKTGS 280 Anopheles gambiae str. ...
EEA45164  276 YTISDIQSLWSEYHTEITAQ.[25].MASFFFSQPRVDFWKFCAEQITGCIQMVVEFAKNIPGFMDLCQNDQIILLKTGC 374 Florida lancelet
CAJ90622  403 QISELLSKTIADAHARTCLF.[16].KLLYYKNMAHEELWLECAQKLTTVIQQIIEFAKMVPGFMKLSQDDQIVLLKAGS 492 German cockroach

Feature 1        #  ## ##       ###         #  #            #                                
1S0X_A    108 LEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGC.[1].DFISFVFEFGKSL.[2].MHLTEDEIALFSAFVLMSAD 179 human
1N4H_A    100 LEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGS.[1].DLVNEAFDFAKNL.[2].LQLTEEEIALFSSAVLISPD 171 Norway rat
1N83_A    108 LEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGC.[1].DFISFVFEFGKSL.[2].MHLTEDEIALFSAFVLMSAD 179 human
NP_990424 300 LEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGS.[1].DLVNEAFDFAKNL.[2].LQLTEEEIALFSSAVLISPD 371 chicken
Q7ZU39    312 LEVVFVRMCRAYNSQNNTVFFDSKYAGPEVFKALGC.[1].DLISSVFEFAKSL.[2].LQLSEDEIGLFSAYVLMSAD 383 zebrafish
CAG11892  354 MEVVLVRMSRFFNTENNTVYFDGKFAGADLFKSLAC.[1].DLITAVFDFAHDM.[2].LKLSEHQLALFSALVLINTD 425 spotted green pufferfish
Q3ZBY9    370 MEVVLVRMCRAYNADNDTVFFEGKYGGVELFRALGC.[1].ELISSIFDFSRSL.[2].LRFSEDEIALYTALVLINAN 441 cattle
Q4H2V2    470 LEVVLVRMARAFNITNQTVLFDEKYTPIETFRSLGC.[1].DLISGMFEMAKSI.[2].LNLTEDQIALFSFAVLITGD 541 Ciona intestinalis
Q5XG07    245 MELLLIRMSRAFNCYNSTIYFEGKYAPLDLFQSLGC.[1].DLISAMFDLCHSL.[2].LNLTEHEMAFFSSMVLLDPS 316 African clawed frog
Q7PWD9    281 FELAIVRMSRLMDLSTNSVLYGDIMLPQEAFYTSDS.[3].KLVACIFETAKSI.[2].LKLTETELALYQSLVLLWPE 354 Anopheles gambiae str. PEST
EEA45164  375 FENLLVRMSREINPNTNAVLFDGKFASIDFFSILGL.[1].DLVSAMYDLGRSV.[2].LKLTEQELALFCAVVLVSAD 446 Florida lancelet
CAJ90622  493 FELAVLRMSRYFDLSQNCVLYADTMLPQDAFYTTET.[3].KLVTCVFEFAKGV.[2].LKLTETELALYSACVLLSAD 566 German cockroach

Feature 1                                                          #                   
1S0X_A    180 .[1].SWLQEKVKIEKLQQKIQLALQHVL.[ 8].ILTKLICKVSTLRALCGRHTEKL.[14].FPPLYKELF 258 human
1N4H_A    172 .[1].AWLLEPRKVQKLQEKIYFALQHVI.[ 8].TLAKLIAKIPTITAVCNLHGEKL.[14].FPPLYKELF 250 Norway rat
1N83_A    180 .[1].SWLQEKVKIEKLQQKIQLALQHVL.[ 8].ILTKLICKVSTLRALCGRHTEKL.[14].FPPLYKELF 258 human
NP_990424 372 .[1].AWLIEPRKVQKLQEKIYFALQHVI.[ 8].TLTKLIAKIPTITALCNLHGEKL.[14].FPPLYKELF 450 chicken
Q7ZU39    384 .[1].SWLQEKTRVEKLQQKIKIALQNLL.[ 8].ILTKLVCKVSTVRMLCRHHMEKL.[14].FPPLYKELF 462 zebrafish
CAG11892  426 .[1].PCLEDRGKVQRVQRTVELGLRHIL.[ 7].LMAKLYQKMAVLRSLCSLHMEKL.[14].FPPLYKELF 503 spotted green pufferfish
Q3ZBY9    442 .[1].PGLQEKRKVEQLQCNLELAFHHHL.[ 3].HRQGILAKLPPKGKLRSLCSQHV.[17].FPPLYKELF 518 cattle
Q4H2V2    542 .[1].PGLWESNRLNKLQSVVLGSLQEMF.[ 9].ILTKLVMNMLNLRNLSRLHSKYF.[11].LPPLYKELF 618 Ciona intestinalis
Q5XG07    317 .[1].PWLQEKEKVENLHVKLELSFRQLL.[ 3].HRESILCKLPQKGRLLSICQLHM.[17].FPPLYKELF 393 African clawed frog
Q7PWD9    355 .[1].NGVRGNTEIQRLFNMSMSAIRQEI.[12].VLDTLLNKIPTFRELSIMHMEAL.[11].FPALYKELF 434 Anopheles gambiae str. PEST
EEA45164  447 .[1].PGLREPMAVEKLQEKIIQALRYQV.[ 9].FLAKILMKMPNLRSVAARHMEEL.[12].FPPLYKELF 524 Florida lancelet
CAJ90622  567 .[1].PGLKGLAEIGRLSQAVLRALRIEL.[13].VYDALLAKVPTLRELSMLHMDAL.[11].FPALHKELF 647 German cockroach

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