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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ECDYSONE RECEPTOR BOUND TO BYI08346
 
Authors :  D. Moras, I. M. L. Billas, C. Browning
Date :  04 Sep 09  (Deposition) - 15 Dec 10  (Release) - 15 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (2x)
Keywords :  Anti-Parallel Alpha-Helices, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Moras, I. M. L. Billas, C. Browning
Adaptability Of The Ecdysone Receptor Bound To Synthetic Ligands
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GENE REGULATION PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 3-264
    Gene: ECR
    Organism Common: TOBACCO BUDWORM MOTH
    Organism Scientific: HELIOTHIS VIRESCENS
    Organism Taxid: 7102
 
Molecule 2 - ECDYSONE RECEPTOR
    Chains: D
    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
    Fragment: RESIDUES 285-532
    Gene: USP
    Mutation: YES
    Organism Common: AMERICAN BOLLWORM,CORN EAR WORM,SCARCE BORDERED STRAW,TOBACCO BUDWORM
    Organism Scientific: HELICOVERPA ARMIGERA
    Organism Taxid: 29058

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
18341Ligand/IonN-[2-(2-CHLOROPHENYL)-4-METHYL-5-(1-METHYLETHYL)-1H-IMIDAZOL-1-YL]-5-METHYL-2,3-DIHYDRO-1,4-BENZODIOXINE-6-CARBOXAMIDE
2EPH1Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
18342Ligand/IonN-[2-(2-CHLOROPHENYL)-4-METHYL-5-(1-METHYLETHYL)-1H-IMIDAZOL-1-YL]-5-METHYL-2,3-DIHYDRO-1,4-BENZODIOXINE-6-CARBOXAMIDE
2EPH2Ligand/IonL-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:230 , VAL A:238 , PRO A:239 , PHE A:242 , LEU A:249 , CYS A:250 , GLY A:328 , LEU A:331 , GLN A:338 , ALA A:339 , GLY A:340 , ILE A:344 , SER A:431 , LEU A:435 , PHE A:438 , LEU A:440 , HOH A:993BINDING SITE FOR RESIDUE EPH A 900
2AC2SOFTWARETHR D:343 , MET D:380 , MET D:381 , VAL D:384 , TYR D:408 , MET D:413 , VAL D:416 , LEU D:420 , GLN D:503 , ASN D:504 , MET D:507 , LEU D:522BINDING SITE FOR RESIDUE 834 D 800

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IXP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IXP)

(-) 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:242
 aligned with Q7SIF6_HELVI | Q7SIF6 from UniProtKB/TrEMBL  Length:264

    Alignment length:256
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253      
         Q7SIF6_HELVI     4 QELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNHAPPI 259
               SCOP domains d3ixpa_ A: Ultraspiracle protein, usp                                                                                                                                                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--------------....eeeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ixp A 206 QELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLT--------------SPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNHAPPI 461
                                   215       225       235       245       255       265       275       285       295       | -         -  |    325       335       345       355       365       375       385       395       405       415       425       435       445       455      
                                                                                                                           303            318                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:220
 aligned with B9UCQ4_HELAM | B9UCQ4 from UniProtKB/TrEMBL  Length:545

    Alignment length:243
                                   296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526   
         B9UCQ4_HELAM   287 VPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKNRKLPPFLEEIWDVA 529
               SCOP domains d3ixpd_ D: automated mat                       ches                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh...-----------------------hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhee....ee........hhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ixp D 287 VPPLTANQKSLIARLVYYQEGYEQ-----------------------MPFRQITEMTILTVQLIVEFAKGLPGFSKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGLEQPSLVEEIQRYYLNTLRVYILNQNSASPRSAVIFGKILGILTEIRTLGMQNSNMCISLKLKNRKLPPFLEEIWDVA 529
                                   296       306   |     -         -       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526   
                                                 310                     334
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 21)

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   (B9UCQ4_HELAM | B9UCQ4)
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: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

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        Q7SIF6_HELVI | Q7SIF6: 1g2n 1r1k 1r20 2r40 4umm

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