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(-) Description

Title :  MINERALOCORTICOID RECEPTOR LIGAND-BINDING DOMAIN WITH SPIRONOLACTONE
 
Authors :  S. Sogabe, N. Habuka
Date :  07 Sep 11  (Deposition) - 28 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A
Keywords :  Nuclear Receptor, Transcription Factor, Activating Mutation, Hypertension, Antagonist, Spironolactone, Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hasui, N. Matsunaga, T. Ora, N. Ohyabu, N. Nishigaki, Y. Imura, Y. Igata, H. Matsui, T. Motoyaji, T. Tanaka, N. Habuka, S. Sogabe, M. Ono, C. S. Siedem, T. P. Tang, C. Gauthier, L. A. De Meese, S. A. Boyd, S. Fukumoto
Identification Of Benzoxazin-3-One Derivatives As Novel, Potent, And Selective Nonsteroidal Mineralocorticoid Receptor Antagonists
J. Med. Chem. V. 54 8616 2011
PubMed-ID: 22074142  |  Reference-DOI: 10.1021/JM2011645

(-) Compounds

Molecule 1 - MINERALOCORTICOID RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentLIGAND-BINDING DOMAIN, UNP RESIDUES 712-984
    GeneNR3C2, MCR, MLR
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SNL1Ligand/IonSPIRONOLACTONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:766 , LEU A:769 , ASN A:770 , ALA A:773 , GLN A:776 , MET A:807 , LEU A:810 , ARG A:817 , PHE A:829 , MET A:845 , MET A:852 , LEU A:938 , PHE A:941 , CYS A:942 , THR A:945 , PHE A:956BINDING SITE FOR RESIDUE SNL A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 12)

Asymmetric/Biological Unit (12, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_031271P759SMCR_HUMANDisease (PHA1A)  ---AP759S
02UniProtVAR_031272L769PMCR_HUMANDisease (PHA1A)  ---AL769P
03UniProtVAR_031273N770KMCR_HUMANDisease (PHA1A)  ---AN770K
04UniProtVAR_031274Q776RMCR_HUMANDisease (PHA1A)  ---AQ776R
05UniProtVAR_031275S805PMCR_HUMANDisease (PHA1A)  ---AS805P
06UniProtVAR_015626S810LMCR_HUMANDisease (EOHSEP)41511344AL810L
07UniProtVAR_031276S815RMCR_HUMANDisease (PHA1A)  ---AS815R
08UniProtVAR_031277S818LMCR_HUMANDisease (PHA1A)  ---AS818L
09UniProtVAR_029311F826YMCR_HUMANPolymorphism13306592AF826Y
10UniProtVAR_015627L924PMCR_HUMANDisease (PHA1A)  ---AL924P
11UniProtVAR_031278E972GMCR_HUMANDisease (PHA1A)  ---AE972G
12UniProtVAR_031279L979PMCR_HUMANDisease (PHA1A)  ---AL979P

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003447211ENSE00002066715chr4:149365850-149365678173MCR_HUMAN-00--
1.3aENST000003447213aENSE00001221601chr4:149358014-1493562561759MCR_HUMAN1-5865860--
1.5aENST000003447215aENSE00001221249chr4:149181269-149181130140MCR_HUMAN586-633480--
1.7bENST000003447217bENSE00001641416chr4:149116013-149115897117MCR_HUMAN633-672400--
1.8aENST000003447218aENSE00001221232chr4:149076052-149075702351MCR_HUMAN672-7891181A:728-78962
1.9aENST000003447219aENSE00001000702chr4:149073764-149073620145MCR_HUMAN789-837491A:789-83749
1.11ENST0000034472111ENSE00001771423chr4:149041439-149041309131MCR_HUMAN837-881451A:837-88145
1.12ENST0000034472112ENSE00001739163chr4:149035412-149035255158MCR_HUMAN881-933531A:881-933 (gaps)53
1.13fENST0000034472113fENSE00002059455chr4:149002650-1489999132738MCR_HUMAN934-984511A:934-98249

(-) 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:249
 aligned with MCR_HUMAN | P08235 from UniProtKB/Swiss-Prot  Length:984

    Alignment length:255
                                   737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977     
            MCR_HUMAN   728 STISRALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQLPKVESGNAKPLYFH 982
               SCOP domains d3vhua_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.hhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..eeehhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhhhhhhhhh------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------S---------PK-----R----------------------------P----L----R--L-------Y-------------------------------------------------------------------------------------------------P-----------------------------------------------G------P--- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.8a  PDB: A:728-789 UniProt: 672-789 [INCOMPLETE]       -----------------------------------------------Exon 1.11  PDB: A:837-881 UniProt: 837-881   ----------------------------------------------------Exon 1.13f  PDB: A:934-982 UniProt: 934-984       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.9a  PDB: A:789-837 UniProt: 789-837       -------------------------------------------Exon 1.12  PDB: A:881-933 (gaps) UniProt: 881-933    ------------------------------------------------- Transcript 1 (2)
                 3vhu A 728 STISRALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVT------GQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLVEIISDQLPKVESGNAKPLYFH 982
                                   737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907|      917       927       937       947       957       967       977     
                                                                                                                                                                                                              908    915                                                                   

   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  (0, 0)

(no "CATH Domain" information available for 3VHU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VHU)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MCR_HUMAN | P08235)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0005496    steroid binding    Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
    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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCR_HUMAN | P082351y9r 1ya3 2a3i 2aa2 2aa5 2aa6 2aa7 2aax 2ab2 2abi 2oax 3vhv 3wff 3wfg 4pf3 4tnt 4uda 4udb 5hcv 5l7e 5l7g 5l7h

(-) Related Entries Specified in the PDB File

2ab2 SAME LIGAND
2oax SAME LIGAND
3vhv