1NAV,1N46,1BSX,2PIN,3D57


Conserved Protein Domain Family
NR_LBD_TR

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cd06935: NR_LBD_TR 
Click on image for an interactive view with Cn3D
The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors.
The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Statistics
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PSSM-Id: 132733
View PSSM: cd06935
Aligned: 12 rows
Threshold Bit Score: 359.898
Threshold Setting Gi: 115732680
Created: 19-Nov-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 20 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                                                                       #  ## ##  #  #   
1NAV_A        17 PEEWDLIHIATEAHRSTnaqgshwkqrrkf----------lpddigqspivsmPDGDKVDLEAFSEFTKIITPAITRVVD 86
1N46_A        13 DEEWELIKTVTEAHVATnaqgshwkqkrkf----------lpedigqapivnaPEGGKVDLEAFSHFTKIITPAITRVVD 82
1BSX_A        15 DEEWELIKTVTEAHVATnaqgshwkqkrkf----------lpedigqapivnaPEGGKVDLEAFSHFTKIITPAITRVVD 84
2PIN_A         8 DEEWELIKTVTEAHVATnaqgshwkqkrkf----------lpedigqapivnaPEGGKVDLEAFSHFTKIITPAITRVVD 77
3D57_A        22 DEEWELIKTVTEAHVATnaqgshwkqkrkf----------lpedigqapivnaPEGGKVDLEAFSHFTKIITPAITRVVD 91
gi 151413583 179 TCPKKVNRYYLNGSPKPgmpvpeaprppvv----------qngvvreadssgaMDDDMVDQDIFSHLAEVITPAIIKVVE 248
gi 13431914  159 AEEWELIHVVTEAHRSTnaqgshwkqkrkf----------lpedigqspmasmPDGDKVDLEAFSEFTKIITPAITRVVD 228
gi 6175061   170 SEEWELIRIVTEAHRSTnaqgshwkqrrkf----------lpedigqspmasmPDGDKVDLEAFSEFTKIITPAITRVVD 239
gi 82274155  223 SDPSGLIPDPLLDSRATsstfpqlltcpilrpgfsrpadappdkigqspvaptSDGDKVDLEAFSEFTKIITPAITRVVD 302
gi 115732680 186 DHEEALIRAILVAHKQTshmyrres---------------------ssgeesePDSKKQKLEDEKPLSEIMTPSIVKVVE 244
gi 586092    216 DEEWELIKTVTEAHVATnaqgshwkqkrkf----------lpedigqapivnaPEGGKVDLEAFSHFTKIITPAITRVVD 285
gi 215273960 141 QEEWEMIRVVTEAHMATnaqgnhwkqkrkflsavg-vkeakpedigsapivnaPEGNKVDIEAFSQFTKIITPAITRVVD 219
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                #  #   #           ###         #  # #      #            
1NAV_A        87 FAKKLPMFsELPCEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMaVKREQLKNGGLGVVSDAIFELGKSLSaFNL 166
1N46_A        83 FAKKLPMFcELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMaVTRGQLKNGGLGVVSDAIFDLGMSLSsFNL 162
1BSX_A        85 FAKKLPMFcELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMaVTRGQLKNGGLGVVSDAIFDLGMSLSsFNL 164
2PIN_A        78 FAKKLPMFcELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMaVTRGQLKNGGLGVVSDAIFRLGMSLSsFNL 157
3D57_A        92 FAKKLPMFcELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMaVTRGQLKNGGLGVVSDAIFRLGMSLSsFNL 171
gi 151413583 249 FAKQIPGFtKLVPDDQVALLKNCCFEVMCLRAASRFDKQRRTITMFGGLtVTKEQVSQGGLGRLAEPLFEFAEGLSqLHL 328
gi 13431914  229 FAKKLPMFsELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMaVKREQLKNGGLGVVSDAIFDLGKSLSaFNL 308
gi 6175061   240 FAKKLPMFsELTCEDQIILLKGCCMEIMSLRAAVRYDPDSETLTLSGEMaVKREQLKNGGLGVVSDAIFDLGRSLAaFNL 319
gi 82274155  303 FAKKLPMFsELPCEDQIILLKGCCMEIMSLRAAMRYDPESETLTLSGEMaVKREQLKNGGLGVVSDAIFDLGKSLAqFNL 382
gi 115732680 245 FAKRIPGFtGLHHDDQILLLKTCCMEIMCLRVAQKFDPDSQKLILSNGLrVGKSDMDHGVLSELIEPIFDFAVSMSrLQL 324
gi 586092    286 FAKKLPMFcELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMaVTRGQLKNGGLGVVSDAIFDLGMSLSsFNL 365
gi 215273960 220 FAKKLPMFcELPCEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLNGEMaVTRGQLKNGGLGVVSDAIFDLGVSLSsFNL 299
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
1NAV_A       167 DDTEVALLQAVLLMSTDRs---------------------------GLLCVDKIEKSQEAYLLAFEHYVNhrKHNIPHFW 219
1N46_A       163 DDTEVALLQAVLLMSSDRp---------------------------GLACVERIEKYQDSFLLAFEHYINyrKHHVTHFW 215
1BSX_A       165 DDTEVALLQAVLLMSSDRp---------------------------GLACVERIEKYQDSFLLAFEHYINyrKHHVTHFW 217
2PIN_A       158 DDTEVALLQAVLLMSSDRp---------------------------GLACVERIEKYQDSFLLAFEHYINyrKHHVTHFW 210
3D57_A       172 DDTEVALLQAVLLMSSDRp---------------------------GLACVERIEKYQDSFLLAFEHYINyrKHHVTHFW 224
gi 151413583 329 DDTEVALLAALLVVADRP----------------------------GVQDQESIDRLQDIILTAYKNYITrqRPHQPVLW 380
gi 13431914  309 DDTEVALLQAVLLMSSDRt---------------------------GLICVDKIEKCQETYLLAFEHYINyrKHNIPHFW 361
gi 6175061   320 DDTEVALLQAVLLMSSDRt---------------------------GLICTDKIEKCQETYLLAFEHYINhrKHNIPHFW 372
gi 82274155  383 DDTEVALLQAVLLMSSGNrrrgrprpspapgstssssssssssdrsGLTCTDKIEKCQETYLLAFEHYINyrKHNIPHFW 462
gi 115732680 325 TETEMALLAAVLLIAGDRp---------------------------GLKEAKLVETLQDSLLTAFQHFINesRPKTPVHW 377
gi 586092    366 DDTEVALLQAVLLMSSDRp---------------------------GLACVERIEKYQDSFLLAFEHYINyrKHHVTHFW 418
gi 215273960 300 DDSEVALLQAVILLSSDRp---------------------------GLTSVERIERCQEEFLLAFEHYINyrKHKVAHFW 352
                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
Feature 1                        #      #            #   
1NAV_A       220 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 259
1N46_A       216 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 255
1BSX_A       218 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 257
2PIN_A       211 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 250
3D57_A       225 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 264
gi 151413583 381 GKILMKVTDLRALSVAHAEQVKLVKMECTNDI-PPLFLEM 419
gi 13431914  362 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 401
gi 6175061   373 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 412
gi 82274155  463 PKLLMKVTDLRMIGACHASRFLHMKVECPNELfPPLFLEV 502
gi 115732680 378 AKILMKITDLRTISARHAERIMCIKLDRPNEI-PQIFLEM 416
gi 586092    419 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 458
gi 215273960 353 PKLLMKVTDLRMIGACHASRFLHMKVECPTELfPPLFLEV 392

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