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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE ESTROGEN-RELATED RECEPTOR GAMMA IN COMPLEX WITH DIETHYLSTILBESTROL
 
Authors :  H. Greschik, R. Flaig, J. P. Renaud, D. Moras
Date :  05 Feb 04  (Deposition) - 08 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4:  B (1x),C (1x)
Biol. Unit 5:  A,D  (1x)
Keywords :  Ligand-Binding Domain, Antagonist Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Greschik, R. Flaig, J. P. Renaud, D. Moras
Structural Basis For The Deactivation Of The Estrogen-Related Receptor {Gamma} By Diethylstilbestrol Or 4-Hydroxytamoxifen And Determinants Of Selectivity.
J. Biol. Chem. V. 279 33639 2004
PubMed-ID: 15161930  |  Reference-DOI: 10.1074/JBC.M402195200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ESTROGEN-RELATED RECEPTOR GAMMA
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneESRRG, NR3B3, ERRG2, ERR3, KIAA0832
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymESTROGEN RECEPTOR RELATED PROTEIN 3, ERR GAMMA-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD
Biological Unit 3 (1x)A (1x)B (1x)C (1x)D (1x)
Biological Unit 4 (1x) B (1x)C (1x) 
Biological Unit 5 (1x)A  D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1DES4Ligand/IonDIETHYLSTILBESTROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1DES2Ligand/IonDIETHYLSTILBESTROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1DES2Ligand/IonDIETHYLSTILBESTROL
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1DES2Ligand/IonDIETHYLSTILBESTROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1DES1Ligand/IonDIETHYLSTILBESTROL
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1DES2Ligand/IonDIETHYLSTILBESTROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:189 , LEU A:268 , ALA A:272 , GLU A:275 , LEU A:309 , VAL A:313 , TYR A:326 , HIS A:434 , PHE A:435 , ILE A:438BINDING SITE FOR RESIDUE DES A 459
2AC2SOFTWAREHOH B:14 , GLU B:275 , LEU B:309 , VAL B:313 , ARG B:316 , TYR B:326 , HIS B:434 , PHE B:435 , ILE B:438BINDING SITE FOR RESIDUE DES B 459
3AC3SOFTWAREHOH C:135 , LEU C:268 , ALA C:272 , GLU C:275 , LEU C:309 , VAL C:313 , ARG C:316 , TYR C:326 , HIS C:434 , PHE C:435 , ILE C:438BINDING SITE FOR RESIDUE DES C 500
4AC4SOFTWAREHOH D:90 , LEU D:265 , ALA D:272 , GLU D:275 , LEU D:309 , VAL D:313 , TYR D:326 , HIS D:434 , PHE D:435 , ILE D:438BINDING SITE FOR RESIDUE DES D 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S9P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S9P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S9P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S9P)

(-) Exons   (0, 0)

(no "Exon" information available for 1S9P)

(-) Sequences/Alignments

Asymmetric 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:215
 aligned with ERR3_MOUSE | P62509 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:215
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442     
           ERR3_MOUSE   233 PYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMH 447
               SCOP domains d1s9pa_ A: Orphan nuclear receptor ERR3                                                                                                                                                                                 SCOP domains
               CATH domains 1s9pA00 A:233-447 Retinoid X Receptor                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeehhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9p A 233 PYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMH 447
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442     

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with ERR3_MOUSE | P62509 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:217
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       
           ERR3_MOUSE   234 YNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLF 450
               SCOP domains d1s9pb_ B: Orphan nuclear receptor ERR3                                                                                                                                                                                   SCOP domains
               CATH domains 1s9pB00 B:234-450 Retinoid X Receptor                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9p B 234 YNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLF 450
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       

Chain C from PDB  Type:PROTEIN  Length:219
 aligned with ERR3_MOUSE | P62509 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:219
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443         
           ERR3_MOUSE   234 YNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLE 452
               SCOP domains d1s9pc_ C: Orphan nuclear receptor ERR3                                                                                                                                                                                     SCOP domains
               CATH domains 1s9pC00 C:234-452 Retinoid X Receptor                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh......eeee..eeehhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9p C 234 YNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLE 452
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443         

Chain D from PDB  Type:PROTEIN  Length:225
 aligned with ERR3_MOUSE | P62509 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:225
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453     
           ERR3_MOUSE   234 YNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEAKV 458
               SCOP domains d1s9pd_ D: Orphan nuclear receptor ERR3                                                                                                                                                                                           SCOP domains
               CATH domains 1s9pD00 D:234-458 Retinoid X Receptor                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eeehhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9p D 234 YNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEAKV 458
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453     

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1S9P)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ERR3_MOUSE | P62509)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0004879    RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding    Combining with a signal 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:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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:0003708    retinoic acid receptor activity    Combining with retinoic acid 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. Retinoic acid is one of the forms of vitamin A.
    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:0001228    transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048384    retinoic acid receptor signaling pathway    The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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
        ERR3_MOUSE | P625091s9q 1vjb

(-) Related Entries Specified in the PDB File

1kv6 CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE ESTROGEN-RELATED RECEPTOR GAMMA (APO-FORM) IN COMPLEX WITH A STEROID RECEPTOR COACTIVATOR 1 PEPTIDE