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: 2-Oct-2020
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 AELEHLAQNISKSHLETCQYlreelqqi---------twqtflqeEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRI 88  human
1N4H_A     10 SEIDRIAQNIIKSHLETCQYtmeelhql---------awqthtyeEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRI 80  Norway rat
1N83_A     18 AELEHLAQNISKSHLETCQYlreelqqi---------twqtflqeEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRI 88  human
NP_990424 210 TEIDRIAQNIIKSHLETCQYtmeelhql---------awqthtyeEIKVYQSKTREALWQQCAIQITHAIQYVVEFAKRI 280 chicken
Q7ZU39    222 DDLEHLSENICKSHLETCQYlreelqps---------nwqtvlqsNLEAYQKKSQEDMWQLCAVKVTEAVQYVVEFAKRI 292 zebrafish
CAG11892  264 CLLDELCASIVRAHRETSQWrveelqgl---------rwklfsreEIQAYQSKSVDEMWQHCAIRLTDAVQYVVEFAKHI 334 spotted green puff...
Q3ZBY9    280 TEIEHLVQNVCKSYRDTCQLrledllrq---------rsnifsreEVAGYQRKSMWEMWGRCAHRLTEAIQYVVEFAKRL 350 cattle
Q4H2V2    380 NISENLVSNICEAYYKTCQYsreelasy---------skavrsqeGTLQFQNMAPDQLWGLCAEKITEAIQHVVEFAKHS 450 Ciona intestinalis
Q5XG07    155 VELDLLMQNVVCAHRETCKFhqenlqvm---------rweafspaEIQSFQQKTMDEMWERCVCHITDAIQYIVEFAKRL 225 African clawed frog
Q7PWD9    192 DINDVLIKTLAEAHANTNHKleivhemf----------rkpqdvsRLLYYKNMTQEELWLDCAEKLTAMIQQIIEFAKLI 261 Anopheles gambiae ...
EEA45164  276 YTISDIQSLWSEYHTEITAQkyrsmvrpkqldiycviswfvyvqdMASFFFSQPRVDFWKFCAEQITGCIQMVVEFAKNI 355 Florida lancelet
CAJ90622  403 QISELLSKTIADAHARTCLFttehihem---------frkpqdlsKLLYYKNMAHEELWLECAQKLTTVIQQIIEFAKMV 473 German cockroach
Feature 1                           #  ## ##       ###         #  #          #                
1S0X_A     89 DGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCe--DFISFVFEFGKSLcsMHLTEDE 166 human
1N4H_A     81 TGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSd--DLVNEAFDFAKNLcsLQLTEEE 158 Norway rat
1N83_A     89 DGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCe--DFISFVFEFGKSLcsMHLTEDE 166 human
NP_990424 281 TGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSd--DLVNEAFDFAKNLcsLQLTEEE 358 chicken
Q7ZU39    293 DGFMELCQNDQIVLLKAGSLEVVFVRMCRAYNSQNNTVFFDSKYAGPEVFKALGCd--DLISSVFEFAKSLnsLQLSEDE 370 zebrafish
CAG11892  335 PGFRMLTQNDQIALLKTGSMEVVLVRMSRFFNTENNTVYFDGKFAGADLFKSLACg--DLITAVFDFAHDMcaLKLSEHQ 412 spotted green puff...
Q3ZBY9    351 PGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNDTVFFEGKYGGVELFRALGCs--ELISSIFDFSRSLsaLRFSEDE 428 cattle
Q4H2V2    451 NAFMSFDQHDQIILLKTGCLEVVLVRMARAFNITNQTVLFDEKYTPIETFRSLGCd--DLISGMFEMAKSIaeLNLTEDQ 528 Ciona intestinalis
Q5XG07    226 NGFMELNPNDQIVLLKAGAMELLLIRMSRAFNCYNSTIYFEGKYAPLDLFQSLGCn--DLISAMFDLCHSLcdLNLTEHE 303 African clawed frog
Q7PWD9    262 PGFMRLSQDDQILLLKTGSFELAIVRMSRLMDLSTNSVLYGDIMLPQEAFYTSDSfemKLVACIFETAKSIteLKLTETE 341 Anopheles gambiae ...
EEA45164  356 PGFMDLCQNDQIILLKTGCFENLLVRMSREINPNTNAVLFDGKFASIDFFSILGLn--DLVSAMYDLGRSVcmLKLTEQE 433 Florida lancelet
CAJ90622  474 PGFMKLSQDDQIVLLKAGSFELAVLRMSRYFDLSQNCVLYADTMLPQDAFYTTETaemKLVTCVFEFAKGVaeLKLTETE 553 German cockroach
Feature 1                                                                          #          
1S0X_A    167 IALFSAFVLMSADrSWLQEKVKIEKLQQKIQLALQHVLqknh-----redgILTKLICKVSTLRALCGRHTEKLmafkai 241 human
1N4H_A    159 IALFSSAVLISPDrAWLLEPRKVQKLQEKIYFALQHVIqknh-----lddeTLAKLIAKIPTITAVCNLHGEKLqvfkqs 233 Norway rat
1N83_A    167 IALFSAFVLMSADrSWLQEKVKIEKLQQKIQLALQHVLqknh-----redgILTKLICKVSTLRALCGRHTEKLmafkai 241 human
NP_990424 359 IALFSSAVLISPDrAWLIEPRKVQKLQEKIYFALQHVIqknh-----lddeTLTKLIAKIPTITALCNLHGEKLqvfkqs 433 chicken
Q7ZU39    371 IGLFSAYVLMSADrSWLQEKTRVEKLQQKIKIALQNLLqknq-----rdegILTKLVCKVSTVRMLCRHHMEKLsafral 445 zebrafish
CAG11892  413 LALFSALVLINTDrPCLEDRGKVQRVQRTVELGLRHILqkdn------qegLMAKLYQKMAVLRSLCSLHMEKLrwfsqr 486 spotted green puff...
Q3ZBY9    429 IALYTALVLINANrPGLQEKRKVEQLQCNLELAFHHHLck----------tHRQGILAKLPPKGKLRSLCSQHVeklqtf 498 cattle
Q4H2V2    529 IALFSFAVLITGDrPGLWESNRLNKLQSVVLGSLQEMFhkths----dppdILTKLVMNMLNLRNLSRLHSKYFlyfkhh 604 Ciona intestinalis
Q5XG07    304 MAFFSSMVLLDPSqPWLQEKEKVENLHVKLELSFRQLLrr----------tHRESILCKLPQKGRLLSICQLHMeklnif 373 African clawed frog
Q7PWD9    342 LALYQSLVLLWPErNGVRGNTEIQRLFNMSMSAIRQEIeanhap-lkgdvtVLDTLLNKIPTFRELSIMHMEALqkfkqd 420 Anopheles gambiae ...
EEA45164  434 LALFCAVVLVSADrPGLREPMAVEKLQEKIIQALRYQVsqthp----aepsFLAKILMKMPNLRSVAARHMEELaalkmq 509 Florida lancelet
CAJ90622  554 LALYSACVLLSADrPGLKGLAEIGRLSQAVLRALRIELernhaipikgdvtVYDALLAKVPTLRELSMLHMDALakfkrs 633 German cockroach
Feature 1                         
1S0X_A    242 y---pdivrlhFPPLYKELF 258 human
1N4H_A    234 h---pdivntlFPPLYKELF 250 Norway rat
1N83_A    242 y---pdivrlhFPPLYKELF 258 human
NP_990424 434 h---pdivntlFPPLYKELF 450 chicken
Q7ZU39    446 y---pemvhtrFPPLYKELF 462 zebrafish
CAG11892  487 y---pltvhslFPPLYKELF 503 spotted green pufferfish
Q3ZBY9    499 qhlhpivvqaaFPPLYKELF 518 cattle
Q4H2V2    605 ------fvnvsLPPLYKELF 618 Ciona intestinalis
Q5XG07    374 rhmypgiawerFPPLYKELF 393 African clawed frog
Q7PWD9    421 ------hpqyvFPALYKELF 434 Anopheles gambiae str. PEST
EEA45164  510 -----spslpeFPPLYKELF 524 Florida lancelet
CAJ90622  634 ------tphleFPALHKELF 647 German cockroach

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