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(-) Description

Title :  CRYSTAL STRUCTURE OF TR-BETA BOUND TO THE SELECTIVE THYROMIMETIC TRIAC
 
Authors :  A. S. Nascimento, S. G. M. Dias, F. M. Nunes, R. Aparicio
Date :  23 Sep 09  (Deposition) - 08 Dec 09  (Release) - 01 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Tr, Triac, Entropy, Deafness, Disease Mutation, Dna-Binding, Metal- Binding, Nucleus, Receptor, Transcription, Transcription Regulation, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Martinez, A. S. Nascimento, F. M. Nunes, K. Phillips, R. Aparicio, S. M. Dias, A. C. Figueira, J. H. Lin, P. Nguyen, J. W. Apriletti, F. A. Neves, J. D. Baxter, P. Webb, M. S. Skaf, I. Polikarpov
Gaining Ligand Selectivity In Thyroid Hormone Receptors Via Entropy.
Proc. Natl. Acad. Sci. Usa V. 106 20717 2009
PubMed-ID: 19926848  |  Reference-DOI: 10.1073/PNAS.0911024106

(-) Compounds

Molecule 1 - THYROID HORMONE RECEPTOR BETA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 202-461, LIGAND BINDING DOMAIN
    GeneTHRB, ERBA2, NR1A2, THR1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNUCLEAR RECEPTOR SUBFAMILY 1 GROUP A MEMBER 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
14HY1Ligand/Ion[4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETICACID
2CAS4Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:272 , ILE A:276 , ALA A:279 , MET A:313 , ARG A:320 , LEU A:330 , ASN A:331 , GLY A:344 , ILE A:353 , HIS A:435 , PHE A:455 , HOH A:473BINDING SITE FOR RESIDUE 4HY A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3JZC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3JZC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (35, 35)

Asymmetric/Biological Unit (35, 35)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_050577D216GTHB_HUMANPolymorphism9865746AD216G
02UniProtVAR_004632A234TTHB_HUMANDisease (GTHR)121918694AA234T
03UniProtVAR_004633R243WTHB_HUMANDisease (GTHR)121918707AR243W
04UniProtVAR_059041A268GTHB_HUMANDisease (GTHR)  ---AA268G
05UniProtVAR_004634R316HTHB_HUMANDisease (PRTH)121918695AR316H
06UniProtVAR_004635A317TTHB_HUMANDisease (GTHR)121918690AA317T
07UniProtVAR_004636R320CTHB_HUMANDisease (GTHR)121918696AR320C
08UniProtVAR_004637R320HTHB_HUMANDisease (GTHR)121918693AR320H
09UniProtVAR_059042N331DTHB_HUMANDisease (GTHR)  ---AN331D
10UniProtVAR_004638G332RTHB_HUMANDisease (GTHR)28999969AG332R
11UniProtVAR_059043A335PTHB_HUMANDisease (GTHR)  ---AA335P
12UniProtVAR_011784T337ITHB_HUMANPolymorphism1054624AT337I
13UniProtVAR_004640R338WTHB_HUMANDisease (GTHR)121918697AR338W
14UniProtVAR_004641Q340HTHB_HUMANDisease (GTHR)121918688AQ340H
15UniProtVAR_059044L341PTHB_HUMANDisease (GTHR)  ---AL341P
16UniProtVAR_004642K342ITHB_HUMANDisease (GTHR)  ---AK342I
17UniProtVAR_004645G345RTHB_HUMANDisease (GTHR)121918686AG345R
18UniProtVAR_004644G345STHB_HUMANDisease (GTHR)121918686AG345S
19UniProtVAR_004643G345VTHB_HUMANDisease (GTHR)28999970AG345V
20UniProtVAR_059045L346FTHB_HUMANDisease (GTHR)  ---AL346F
21UniProtVAR_004646G347ETHB_HUMANDisease (GTHR)28999971AG347E
22UniProtVAR_004647V348ETHB_HUMANDisease (GTHR)  ---AV348E
23UniProtVAR_004648T426ITHB_HUMANDisease (GTHR)  ---AT426I
24UniProtVAR_058508R429QTHB_HUMANDisease (PRTH)  ---AR429Q
25UniProtVAR_059046I431MTHB_HUMANDisease (GTHR)  ---AI431M
26UniProtVAR_004649R438HTHB_HUMANDisease (GTHR)121918698AR438H
27UniProtVAR_004650M442VTHB_HUMANDisease (GTHR)121918691AM442V
28UniProtVAR_004651K443ETHB_HUMANDisease (GTHR)121918692AK443E
29UniProtVAR_004652C446RTHB_HUMANDisease (GTHR)121918703AC446R
30UniProtVAR_059047P447TTHB_HUMANDisease (GTHR)  ---AP447T
31UniProtVAR_004653P453HTHB_HUMANDisease (GTHR)121918687AP453H
32UniProtVAR_059048P453LTHB_HUMANDisease (GTHR)  ---AP453L
33UniProtVAR_004654P453STHB_HUMANDisease (GTHR)  ---AP453S
34UniProtVAR_004655P453TTHB_HUMANDisease (GTHR)28933408AP453T
35UniProtVAR_059049F459CTHB_HUMANDisease (GTHR)121918702AF459C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3JZC)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2gENST000003966712gENSE00001687497chr3:24536266-2453617889THB_HUMAN-00--
1.5ENST000003966715ENSE00001395906chr3:24378862-2437879172THB_HUMAN-00--
1.7aENST000003966717aENSE00001612462chr3:24338862-24338717146THB_HUMAN-00--
1.8bENST000003966718bENSE00001397913chr3:24270492-2427042964THB_HUMAN1-880--
1.10cENST0000039667110cENSE00001693312chr3:24231825-24231565261THB_HUMAN8-95880--
1.12eENST0000039667112eENSE00001642867chr3:24193981-24193881101THB_HUMAN95-128340--
1.13bENST0000039667113bENSE00001073518chr3:24188313-24188166148THB_HUMAN129-178500--
1.14ENST0000039667114ENSE00001073519chr3:24185197-24184992206THB_HUMAN178-246691A:202-24645
1.15ENST0000039667115ENSE00001073517chr3:24174953-24174807147THB_HUMAN247-295491A:247-295 (gaps)49
1.16ENST0000039667116ENSE00001718132chr3:24169248-24168990259THB_HUMAN296-382871A:296-38287
1.17dENST0000039667117dENSE00001406950chr3:24164616-241586515966THB_HUMAN382-461801A:382-46079

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:248
 aligned with THB_HUMAN | P10828 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:259
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451         
            THB_HUMAN   202 EELQKSIGHKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPEDIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEVFE 460
               SCOP domains d3jzca_ A: Thyroid hormone receptor beta (TR-beta)                                                                                                                                                                                                                  SCOP domains
               CATH domains 3jzcA00 A:202-460 Retinoid X Receptor                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------Hormone_recep-3jzcA01 A:264-445                                                                                                                                                       --------------- Pfam domains
         Sec.struct. author hhhhhhhh.....hhhhhhhhhhhhhhhhh............ee.......-----------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........eee...eeehhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) --------------G-----------------T--------W------------------------G-----------------------------------------------HT--C----------DR--P-IW-HPI--RFEE-----------------------------------------------------------------------------I--Q-M------H---VE--RT-----H-----C- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------H------------------------S-----------------------------------------------------------------------------------------------------------L------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -----------------------------------------------------------------------------------------------------------------------------------------------V-----------------------------------------------------------------------------------------------------------S------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------- SAPs(SNPs) (4)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.14  PDB: A:202-246 UniProt: 178-246   Exon 1.15  PDB: A:247-295 (gaps) UniProt: 247-295Exon 1.16  PDB: A:296-382 UniProt: 296-382                                             ------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.17d  PDB: A:382-460 UniProt: 382-461 [INCOMPLETE]                        Transcript 1 (2)
                 3jzc A 202 EELQKSIGHKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPEDIGQ-----------VDLEAFSHFTKIITPAITRVVDFAKKLPMFcELPcEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLAcVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGAcHASRFLHMKVECPTELFPPLFLEVFE 460
                                   211       221       231       241       251|        -  |    271       281       291  |   |301       311       321       331       341       351       361       371       381      |391       401       411       421       431  |    441       451         
                                                                            252         264                           294-CAS                                                                                       388-CAS                                       434-CAS                      
                                                                                                                          298-CAS                                                                                                                                                              

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (THB_HUMAN | P10828)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003707    steroid hormone receptor activity    Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function.
    GO:0070324    thyroid hormone binding    Interacting selectively and non-covalently with thyroxine (T4) or triiodothyronine (T3), tyrosine-based hormones produced by the thyroid gland.
    GO:0004887    thyroid hormone receptor activity    Combining with thyroid hormone and transmitting the signal to the transcriptional machinery by interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0060509    Type I pneumocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a Type I pneumocyte. A type I pneumocyte is a flattened cell with greatly attenuated cytoplasm and a paucity of organelles.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0008050    female courtship behavior    The behavior of a female, for the purpose of attracting a sexual partner.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    GO:0007621    negative regulation of female receptivity    Any process that stops, prevents or reduces the receptiveness of a female to male advances.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0008016    regulation of heart contraction    Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        THB_HUMAN | P108281bsx 1n46 1nax 1nq0 1nq1 1nq2 1nuo 1q4x 1r6g 1xzx 1y0x 2j4a 2nll 2pin 3d57 3gws 3imy 4zo1

(-) Related Entries Specified in the PDB File

3jzb