3CJW


Conserved Protein Domain Family
NR_LBD_COUP-TF

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cd06948: NR_LBD_COUP-TF 
Click on image for an interactive view with Cn3D
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family
The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well cons erved 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: 132746
View PSSM: cd06948
Aligned: 12 rows
Threshold Bit Score: 320.942
Threshold Setting Gi: 51860121
Created: 19-Nov-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
putative ligandputative
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:putative ligand binding site [chemical binding site]
Evidence:
  • Comment:predicted based on homologous proteins.
  • Citation:PMID 9744270

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                          ##   #                                 #   #  
3CJW_A         7 YLSGYISLLLRAEPYPTsrfgsqcmqpnnimgIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLN 86
gi 170587670 291 HVSSIVTHLIHAEPYPPiacsss----sssigMDNIYEFGAKLLFSAVEWAKNIPFFNELSDTDQLTLLRASWAELFVIN 366
gi 76364250   99 FLSGYISLLLRAEPYPTsryaqcm-qtnsvmgIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRMCWSELFVLN 177
gi 84617148  117 YLSSFISLLLRAEPYPPsryaqcv-qqnnimgIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLN 195
gi 82200945  152 PVSELISQLLRAEPYPAsrygsqyaqqgsvmgIDNICELAARLLFSTVEWSRNIPYFPELAMADQVSLLRLSWSELFVLS 231
gi 123233077 173 YLSGYISLLLRAEPYPTsrygsqcmqpnnimgIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLN 252
gi 45383323  173 YLSGYISLLLRAEPYPTsrfgsqcmqpnnimgIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLN 252
gi 118343705 179 YMSGYISMLLRAEPYPTsrfalqcpvpnqimgIDNICELAARLLFSAVEWARNIPFFPELQVTDQVAMLKWVWSELFVLN 258
gi 21744271  307 YLSSYISLLLRAEPYPTsrygqcm-qpnnimgIDNICELAARLLFSAVEWAKNIPFFPELQVTDQVALLRLVWSELFVLN 385
gi 74938424  131 FLSGFISLLLRAEPYPTtrfqqgmnmpcgimgIENICELAARLLFSAVEWARNIPFFPDLAVTDQVALLRLVWSELFVLN 210
gi 156387699 130 FYSSYITLLLRADTIARyqqsltl--pcningLENTPELAARLLVSAVEWAKNIPFYSDLPLPDQAVLLRSCWSELFTLN 207
gi 51860121   86 IANYSNVLSARLQQQQQnqylsq----nnlfgGDSIYEMATRLLFNAVEWARNVPFFSALPTSDQIALLKSSWSELYILS 161
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        #             #                            #                                    
3CJW_A        87 AAQCSmPLHVAPLLAAAGLHASpmsa--------drvVAFMDHIRIFQEQVEKLKaLHVDSAEYSCLKAIVLFTSDa-cG 157
gi 170587670 367 AAQFGmPVHVAPLLAASGLHSSpplp-------tdqlVVFMDRIRVFQGQIERLKaLQMDLAEFCSLKAVILFSVDc-cG 438
gi 76364250  178 ASQCSmPLHVAPLLAASGLHASpmsa--------drvVAFMDHIRIFQEQVEKLKaLHVDSAEYSCIKAIVLFTSTdacG 249
gi 84617148  196 ASQCSmPLHVAPLLAAAGLHASpmaa--------drvVAFMDHIRIFQEQVEKLKaLQVDAAEYSCLKAIVLFTTDa-cG 266
gi 82200945  232 AAQSAlPLHMAPLLAAAGFHASpmsa--------drvVSFMDQIRLFQDQVEKLNrLQVDSAEYACLKAIALFTSDa-cG 302
gi 123233077 253 AAQCSmPLHVAPLLAAAGLHASpmsa--------drvVAFMDHIRIFQEQVEKLKaLHVDSAEYSCIKAIVLFTSDa-cG 323
gi 45383323  253 AAQCSmPLHVAPLLAAAGLHASpmsa--------drvVAFMDHIRIFQEQVEKLKaLHVDSAEYSCLKAIVLFTSDa-cG 323
gi 118343705 259 AAQSHmPLHVAPLLAAAGLHTSmsa---------drvMTFMDHIRIFQEQVERLKsLHVDSAEYSCLKAIVLFTADs-hG 328
gi 21744271  386 ASQCSmPLHVAPLLAAAGLHASpmaa--------drvVAFMDHIRIFQEQVEKLKaLHVDSAEYSCLKAIVLFTTDa-cG 456
gi 74938424  211 AAQCPmPLQVAPLLASAGIHSNhmsp--------drmVTFMDNVRIFQEQIEKYRnLHVDAAEFACLKAIVLFTSDa-sG 281
gi 156387699 208 AAQHCsPFHISPTLTSNSSGFAgngggylntrvmsafDCQNNNMKLFEEQVEKLKnMHIDSAEFACLKAIVLFNPDs-qG 286
gi 51860121  162 TSQHCiAFQINARALTSEQNLSeikk--------rseGANEASVKMFEELVERFKnLQTDAAEFSCLKALVLFNPDs-pG 232
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
3CJW_A       158 LSDVAHVESLQEKSQCALEEYVRSQYPNQp--tRFGKLLLRLPSLRTVSSSVIEQLFFVRLVgktpieTLIRDMLLSGs- 234
gi 170587670 439 LNDVIRVETIQEKVQSALEEYCRTQKQLQv--gRFGRLLLRLPSLRSISASVIEQLFFVKLVgetpieFLLRDMLRTQne 516
gi 76364250  250 LSDAAHIEALQEKSQCALEEYVRSQYPNQp--nRFGKLLLRLPSLRTVSSHVIEQLFFVRLVgktpieTLIRDMLLSGs- 326
gi 84617148  267 LSDVAHIESLQEKSQCALEEYCRTQYPNRp--tRFGKLLLRLPSLRTVSSQVIEQLFFVRLVgktpieTLIRDMLLSGs- 343
gi 82200945  303 LTDPAHVESLQEKAQVALTEYVRAQYPSQp--qRFGRLLLRLPALRAVPASLISQLFFMRLVgktpieTLIRDMLLSGs- 379
gi 123233077 324 LSDAAHIESLQEKSQCALEEYVRSQYPNQp--sRFGKLLLRLPSLRTVSSSVIEQLFFVRLVgktpieTLIRDMLLSGs- 400
gi 45383323  324 LSDVAHVESLQEKSQCALEEYVRSQYPNQp--tRFGKLLLRLPSLRTVSSSVIEQLFFVRLVgktpieTLIRDMLLSGs- 400
gi 118343705 329 LSDMTHIESVQEKSQCALEEYVRHQYPNQp--sRFGKLLLRLPSLRTVSASAIEQLFFVRLVgktpieTLIRDMLLSGs- 405
gi 21744271  457 LSDVTHIESLQEKSQCALEEYCRTQYPNQp--tRFGKLLLRLPSLRTVSSQVIEQLFFVRLVgktpieTLIRDMLLSGn- 533
gi 74938424  282 LTDPQYIESLQEKTQCALEEYTRNQYPNQp--tRFGKLLLRLPSLRSINSSIVEQLFFVRLVgktpidTLLRDMLLSGt- 358
gi 156387699 287 LSEPAQVENLQDRTQSALEDYIRTQYPNQt--tRFGKLLLRLPALRLLRPVSVENLFFSRLSmgntvdSLLNDMLLSGlg 364
gi 51860121  233 LGNPSLIENLQEKAQSALEDYLRQQNATQsyhnRFGKLLLRLPALSLIRPATIEALFFPRHHgsqnidSLVGSMLLYGlg 312
                        250
                 ....*....|....
Feature 1                      
3CJW_A       235 -----sFNWPYMAI 243
gi 170587670 517 nv-ikpFVWPCQLR 529
gi 76364250  327 -----sFSWPYMTM 335
gi 84617148  344 -----sFNWPYMPL 352
gi 82200945  380 -----sFNWPYSSG 388
gi 123233077 401 -----sFNWPYMSI 409
gi 45383323  401 -----sFNWPYMSI 409
gi 118343705 406 -----sYGWPYHMT 414
gi 21744271  534 -----sFSWPYLPS 542
gi 74938424  359 -----pTSWPYLPC 367
gi 156387699 365 -----gGVVPWLPG 373
gi 51860121  313 snnntsFVNNGIPA 326

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