2HBH,1S0Z


Conserved Protein Domain Family
NR_LBD_VDR

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cd06933: NR_LBD_VDR 
Click on image for an interactive view with Cn3D
The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily
The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR 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: 132731
View PSSM: cd06933
Aligned: 4 rows
Threshold Bit Score: 449.808
Threshold Setting Gi: 146386497
Created: 1-Dec-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
ligand bindingcoactivator
Conserved site includes 19 residues -Click on image for an interactive view with Cn3D
Feature 1:ligand binding site [chemical binding site]
Evidence:
  • Structure:1HBH_a, zebrafish VDR binds to ligand anolog 21-nor-calcitriol-20(22),23-diyne, contacts at 4A
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                           #   #                                                        
2HBH_A         5 LSDEQMQIINSLVEAHHKTYDdSYSDFVRFRPPVRegpvtrsasraaslhslsdassdsfnhspes-----vdtklnfsn 79  zebrafish
1S0Z_A        11 LSEEQQRIIAILLDAHHKTYDpTYSDFCQFRPPVRvndgggs-------------------------------------- 52  human
NP_001079288 125 ISDEQQKMIDILLEAHRKTFDtTYSDFNKFRPPVRenvdpfrritrsssvhtqgspsedsdvfts-------spdssehg 197 African clawed ...
O42392       147 LSEEQQKVIDTLLEAHHKTFDtTYSDFNKFRPPVRskfssrmathsssvvsqdfssedsndvfgsdafaafpepmepqmf 226 chicken
Feature 1                                #  #  ##  #                                 #  ##  #    
2HBH_A        80 llmmyqdsgspdsseedqqsrLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLE 159 zebrafish
1S0Z_A        53 --------------vtlelsqLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMD 118 human
NP_001079288 198 ffsaslfgqfeyssmggksgeLSMLPHIADLVSYSIQKIIGFAKMIPGFRDLIAEDQIALLKSSVIEVIMLRSNQSFSLD 277 African clawed ...
O42392       227 snldlseesdespsmnielphLPMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQSFTME 306 chicken
Feature 1           # #           #  # #                                                         
2HBH_A       160 DMSWSCGGPDFKYcinDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDV 239 zebrafish
1S0Z_A       119 DMSWTCGNQDYKYrvsDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNT 198 human
NP_001079288 278 DMSWTCGSEDFKYkvdDVTQAGHNMELLEPLVKFQVGLKKLDLHEEEHVLLMAICILSPDRPGLQDKALVESIQDRLSST 357 African clawed ...
O42392       307 DMSWTCGSNDFKYkvsDVTQAGHSMDLLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDTSLVESIQDRLSDI 386 chicken
Feature 1                                          #   #  #                      
2HBH_A       240 LQAYIRiq--hPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV 301 zebrafish
1S0Z_A       199 LQTYIRcrhppPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFGNEI 262 human
NP_001079288 358 LQTYILckhppPGSRLLYAKMIQKLADLRSLNEEHSKQYRSISFLPEHSMKLTPLMLEVFSDEI 421 African clawed frog
O42392       387 LQTYIRcrhppPGSRLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPEHSMQLTPLVLEVFGNEI 450 chicken

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