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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAINS OF THE HETERODIMER ECR/USP BOUND TO PONASTERONE A
 
Authors :  I. M. L. Billas, T. Iwema, J. -M. Garnier, A. Mitschler, N. Rochel, D. Moras, Structural Proteomics In Europe (Spine)
Date :  24 Sep 03  (Deposition) - 18 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  A,D  (2x)
Keywords :  Nuclear Receptor, Transcription Regulation, Heterodimer, Alpha-Helical Sandwich, Structural Proteomics In Europe, Spine, Structural Genomics, Hormone/Growth Factor Receptor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. M. L. Billas, T. Iwema, J. M. Garnier, A. Mitschler, N. Rochel, D. Moras
Structural Adaptability In The Ligand-Binding Pocket Of The Ecdysone Hormone Receptor.
Nature V. 426 91 2003
PubMed-ID: 14595375  |  Reference-DOI: 10.1038/NATURE02112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ECDYSONE RECEPTOR
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HORMONE BINDING DOMAIN
    Gene: ECR OR NR1H1
    Organism Common: TOBACCO BUDWORM
    Organism Scientific: HELIOTHIS VIRESCENS
    Organism Taxid: 7102
    Synonym: ECDYSTEROID RECEPTOR, 20-HYDROXY-ECDYSONE RECEPTOR, 20E RECEPTOR, HVECR
 
Molecule 2 - ULTRASPIRACLE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PACYC11B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: TOBACCO BUDWORM
    Organism Scientific: HELIOTHIS VIRESCENS
    Organism Taxid: 7102

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (1x): AD
Biological Unit 2 (2x): AD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2P1A1Ligand/Ion2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2P1A1Ligand/Ion2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1EPH2Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
2P1A2Ligand/Ion2,3,14,20,22-PENTAHYDROXYCHOLEST-7-EN-6-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU D:309 , GLN D:310 , ILE D:339 , MET D:342 , THR D:343 , THR D:346 , ARG D:383 , VAL D:384 , ARG D:387 , LEU D:396 , PHE D:397 , ALA D:398 , TYR D:408 , MET D:413 , VAL D:416 , LEU D:420 , ASN D:504BINDING SITE FOR RESIDUE P1A D 3000
2AC2SOFTWARELEU A:230 , VAL A:238 , PRO A:239 , PHE A:242 , LEU A:249 , ASN A:287 , LEU A:290 , MET A:323 , LEU A:331 , GLN A:338 , ALA A:339 , SER A:431 , HIS A:434 , PHE A:438 , LEU A:440BINDING SITE FOR RESIDUE EPH A 4000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R1K)

(-) Exons   (0, 0)

(no "Exon" information available for 1R1K)

(-) 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:241
 aligned with Q7SIF6_HELVI | Q7SIF6 from UniProtKB/TrEMBL  Length:264

    Alignment length:251
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252 
         Q7SIF6_HELVI     3 VQELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALR 253
               SCOP domains d1r1ka_ A: Ultraspiracle protein, usp                                                                                                                                                                                                                       SCOP domains
               CATH domains 1r1kA00 A:205-455 Retinoid X Receptor                                                                                                                                                                                                                       CATH domains
               Pfam domains -----------------------Hormone_recep-1r1kA01 A:228-441                                                                                                                                                                                       -------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....----------.......eee.....eeehhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r1k A 205 VQELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTE----------RTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALR 455
                                   214       224       234       244       254       264       274       284       294       304         -|      324       334       344       354       364       374       384       394       404       414       424       434       444       454 
                                                                                                                             304        315                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:236
 aligned with ECR_HELVI | O18473 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:240
                                   317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547
            ECR_HELVI   308 VPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRGAVIFGEILGILTEIRTLGMQNSNMCISLKLKNRKLPPFLEEIWDVA 547
               SCOP domains d1r1kd_ D: Ecdysone receptor                                                                                                                                                                                                                     SCOP domains
               CATH domains 1r1kD00 D:287-529 Retinoid X Receptor                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------Hormone_r    ecep-1r1kD01 D:315-515                                                                                                                                                                   -------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh..hhhhhhhhh...----..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....eeee...eeehhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1r1k D 287 VPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTW----DSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKNRKLPPFLEEIWDVA 529
                                   296       306       316      |  - |     339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529
                                                              323  331
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Hormone_recep] (290)

(-) Gene Ontology  (14, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7SIF6_HELVI | Q7SIF6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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: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:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    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.

Chain D   (ECR_HELVI | O18473)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004884    ecdysteroid hormone receptor activity    Combining with an ecdysteroid 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: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:0035076    ecdysone receptor-mediated signaling pathway    The series of molecular signals generated by ecdysone binding to the ecdysone receptor complex.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043401    steroid hormone mediated signaling pathway    A series of molecular signals mediated by a steroid hormone binding to a receptor.
    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
        ECR_HELVI | O18473: 1r20 2r40 4umm
UniProtKB/TrEMBL
        Q7SIF6_HELVI | Q7SIF6: 1g2n 1r20 2r40 3ixp 4umm

(-) Related Entries Specified in the PDB File

1r20 RELATED ID: IGBMC-0090-000 RELATED DB: TARGETDB