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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                         ###                                      #  ## ##  #           
1S0X_A        18 AELEHLAQNISKSHLETCQYlreelqqi---------twqtflqeEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRI 88
1N4H_A        10 SEIDRIAQNIIKSHLETCQYtmeelhql---------awqthtyeEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRI 80
1N83_A        18 AELEHLAQNISKSHLETCQYlreelqqi---------twqtflqeEIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRI 88
gi 45384158  210 TEIDRIAQNIIKSHLETCQYtmeelhql---------awqthtyeEIKVYQSKTREALWQQCAIQITHAIQYVVEFAKRI 280
gi 82209529  222 DDLEHLSENICKSHLETCQYlreelqps---------nwqtvlqsNLEAYQKKSQEDMWQLCAVKVTEAVQYVVEFAKRI 292
gi 47225409  264 CLLDELCASIVRAHRETSQWrveelqgl---------rwklfsreEIQAYQSKSVDEMWQHCAIRLTDAVQYVVEFAKHI 334
gi 122140854 280 TEIEHLVQNVCKSYRDTCQLrledllrq---------rsnifsreEVAGYQRKSMWEMWGRCAHRLTEAIQYVVEFAKRL 350
gi 122049632 380 NISENLVSNICEAYYKTCQYsreelasy---------skavrsqeGTLQFQNMAPDQLWGLCAEKITEAIQHVVEFAKHS 450
gi 82180196  155 VELDLLMQNVVCAHRETCKFhqenlqvm---------rweafspaEIQSFQQKTMDEMWERCVCHITDAIQYIVEFAKRL 225
gi 74920801  192 DINDVLIKTLAEAHANTNHKleivhemf----------rkpqdvsRLLYYKNMTQEELWLDCAEKLTAMIQQIIEFAKLI 261
gi 210097029 276 YTISDIQSLWSEYHTEITAQkyrsmvrpkqldiycviswfvyvqdMASFFFSQPRVDFWKFCAEQITGCIQMVVEFAKNI 355
gi 114049537 403 QISELLSKTIADAHARTCLFttehihem---------frkpqdlsKLLYYKNMAHEELWLECAQKLTTVIQQIIEFAKMV 473
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                              #  ## ##       ###         #  #          #                
1S0X_A        89 DGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCe--DFISFVFEFGKSLcsMHLTEDE 166
1N4H_A        81 TGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSd--DLVNEAFDFAKNLcsLQLTEEE 158
1N83_A        89 DGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLGCe--DFISFVFEFGKSLcsMHLTEDE 166
gi 45384158  281 TGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALGSd--DLVNEAFDFAKNLcsLQLTEEE 358
gi 82209529  293 DGFMELCQNDQIVLLKAGSLEVVFVRMCRAYNSQNNTVFFDSKYAGPEVFKALGCd--DLISSVFEFAKSLnsLQLSEDE 370
gi 47225409  335 PGFRMLTQNDQIALLKTGSMEVVLVRMSRFFNTENNTVYFDGKFAGADLFKSLACg--DLITAVFDFAHDMcaLKLSEHQ 412
gi 122140854 351 PGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNDTVFFEGKYGGVELFRALGCs--ELISSIFDFSRSLsaLRFSEDE 428
gi 122049632 451 NAFMSFDQHDQIILLKTGCLEVVLVRMARAFNITNQTVLFDEKYTPIETFRSLGCd--DLISGMFEMAKSIaeLNLTEDQ 528
gi 82180196  226 NGFMELNPNDQIVLLKAGAMELLLIRMSRAFNCYNSTIYFEGKYAPLDLFQSLGCn--DLISAMFDLCHSLcdLNLTEHE 303
gi 74920801  262 PGFMRLSQDDQILLLKTGSFELAIVRMSRLMDLSTNSVLYGDIMLPQEAFYTSDSfemKLVACIFETAKSIteLKLTETE 341
gi 210097029 356 PGFMDLCQNDQIILLKTGCFENLLVRMSREINPNTNAVLFDGKFASIDFFSILGLn--DLVSAMYDLGRSVcmLKLTEQE 433
gi 114049537 474 PGFMKLSQDDQIVLLKAGSFELAVLRMSRYFDLSQNCVLYADTMLPQDAFYTTETaemKLVTCVFEFAKGVaeLKLTETE 553
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                             #          
1S0X_A       167 IALFSAFVLMSADrSWLQEKVKIEKLQQKIQLALQHVLqknh-----redgILTKLICKVSTLRALCGRHTEKLmafkai 241
1N4H_A       159 IALFSSAVLISPDrAWLLEPRKVQKLQEKIYFALQHVIqknh-----lddeTLAKLIAKIPTITAVCNLHGEKLqvfkqs 233
1N83_A       167 IALFSAFVLMSADrSWLQEKVKIEKLQQKIQLALQHVLqknh-----redgILTKLICKVSTLRALCGRHTEKLmafkai 241
gi 45384158  359 IALFSSAVLISPDrAWLIEPRKVQKLQEKIYFALQHVIqknh-----lddeTLTKLIAKIPTITALCNLHGEKLqvfkqs 433
gi 82209529  371 IGLFSAYVLMSADrSWLQEKTRVEKLQQKIKIALQNLLqknq-----rdegILTKLVCKVSTVRMLCRHHMEKLsafral 445
gi 47225409  413 LALFSALVLINTDrPCLEDRGKVQRVQRTVELGLRHILqkdn------qegLMAKLYQKMAVLRSLCSLHMEKLrwfsqr 486
gi 122140854 429 IALYTALVLINANrPGLQEKRKVEQLQCNLELAFHHHLck----------tHRQGILAKLPPKGKLRSLCSQHVeklqtf 498
gi 122049632 529 IALFSFAVLITGDrPGLWESNRLNKLQSVVLGSLQEMFhkths----dppdILTKLVMNMLNLRNLSRLHSKYFlyfkhh 604
gi 82180196  304 MAFFSSMVLLDPSqPWLQEKEKVENLHVKLELSFRQLLrr----------tHRESILCKLPQKGRLLSICQLHMeklnif 373
gi 74920801  342 LALYQSLVLLWPErNGVRGNTEIQRLFNMSMSAIRQEIeanhap-lkgdvtVLDTLLNKIPTFRELSIMHMEALqkfkqd 420
gi 210097029 434 LALFCAVVLVSADrPGLREPMAVEKLQEKIIQALRYQVsqthp----aepsFLAKILMKMPNLRSVAARHMEELaalkmq 509
gi 114049537 554 LALYSACVLLSADrPGLKGLAEIGRLSQAVLRALRIELernhaipikgdvtVYDALLAKVPTLRELSMLHMDALakfkrs 633
                        250       260
                 ....*....|....*....|
Feature 1                            
1S0X_A       242 y---pdivrlhFPPLYKELF 258
1N4H_A       234 h---pdivntlFPPLYKELF 250
1N83_A       242 y---pdivrlhFPPLYKELF 258
gi 45384158  434 h---pdivntlFPPLYKELF 450
gi 82209529  446 y---pemvhtrFPPLYKELF 462
gi 47225409  487 y---pltvhslFPPLYKELF 503
gi 122140854 499 qhlhpivvqaaFPPLYKELF 518
gi 122049632 605 ------fvnvsLPPLYKELF 618
gi 82180196  374 rhmypgiawerFPPLYKELF 393
gi 74920801  421 ------hpqyvFPALYKELF 434
gi 210097029 510 -----spslpeFPPLYKELF 524
gi 114049537 634 ------tphleFPALHKELF 647

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