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(-) Description

Title :  THE CRYO-EM STRUCTURE OF THE PALINDROMIC DNA-BOUND USP-ECR NUCLEAR RECEPTOR REVEALS AN ASYMMETRIC ORGANIZATION WITH ALLOSTERIC DOMAIN POSITIONING
 
Authors :  M. Maletta, I. Orlov, D. Moras, I. M. L. Billas, B. P. Klaholz
Date :  19 May 14  (Deposition) - 25 Jun 14  (Release) - 02 Jul 14  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  11.60
Chains :  Asym./Biol. Unit :  A,C,D,E,F,G
Keywords :  Nuclear Receptor, Transcription, Ecdysone, Usp-Ecr, Dna Response Element, Allostery, Cryo Electron Microscopy (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Maletta, I. Orlov, D. Moras, I. M. L. Billas, B. P. Klaholz
The Palindromic Dna-Bound Usp-Ecr Nuclear Receptor Adopts An Asymmetric Organization With Allosteric Domain Positioning.
Nat. Commun. V. 5 4139 2014
PubMed-ID: 24942373  |  Reference-DOI: 10.1038/NCOMMS5139

(-) Compounds

Molecule 1 - ECR-USP
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Organ: NUCLEOUS
    Organism Common: TOBACCO BUDWORM
    Organism Scientific: HELIOTHIS VIRESCENS
    Organism Taxid: 7102
 
Molecule 2 - 5'-D(*CP*AP*AP*GP*GP*GP*TP*TP*CP*AP*AP*TP*GP*CP *AP*CP*TP*TP*GP*TP)-3'
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - 5'-D(*DGP*AP*CP*AP*AP*GP*TP*GP*CP*AP*TP*TP*GP*DAP *AP*CP*CP*CP*TP*T)-3'
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - ECDYSONE RECEPTOR
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Organ: NUCLEOUS
    Organism Scientific: HELIOTHIS VIRESCENS
    Organism Taxid: 7102
    Synonym: 20-HYDROXY-ECDYSONE RECEPTOR, 20E RECEPTOR, ECRH, ECDYSTEROID RECEPTOR, HVECR, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP H MEMBER 1
 
Molecule 5 - GENE REGULATION PROTEIN
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Organ: NUCLEOUS
    Organism Common: TOBACCO BUDWORM
    Organism Scientific: HELIOTHIS VIRESCENS
    Organism Taxid: 7102
    Synonym: ECR-USP
 
Molecule 6 - ECDYSONE RECEPTOR
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Organ: NUCLEOUS
    Organism Common: TOBACCO BUDWORM
    Organism Scientific: HELIOTHIS VIRESCENS
    Organism Taxid: 7102
    Synonym: 20-HYDROXY-ECDYSONE RECEPTOR, 20E RECEPTOR, ECRH, ECDYSTEROID RECEPTOR, HVECR, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP H MEMBER 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ACDEFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological 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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU G:309 , GLN G:310 , ILE G:339 , MET G:342 , THR G:343 , THR G:346 , ARG G:383 , VAL G:384 , ARG G:387 , LEU G:396 , PHE G:397 , ALA G:398 , TYR G:408 , MET G:413 , VAL G:416 , LEU G:420 , ASN G:504BINDING SITE FOR RESIDUE P1A G1530
2AC2SOFTWARELEU F:230 , VAL F:238 , PRO F:239 , PHE F:242 , LEU F:249 , ASN F:287 , LEU F:290 , MET F:323 , LEU F:331 , GLN F:338 , ALA F:339 , SER F:431 , HIS F:434 , PHE F:438 , LEU F:440BINDING SITE FOR RESIDUE EPH F1456

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UMM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro F:268 -His F:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UMM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UMM)

(-) Exons   (0, 0)

(no "Exon" information available for 4UMM)

(-) 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:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............ee..ee.hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4umm A 110 KHLCSICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYACREERNCIIDKRQRNRCQYCRYQKCLACGMKREAVQEER 187
                                   119       129       139       149       159       169       179        


Chain C from PDB  Type:DNA  Length:20
                                                    
                 4umm C   1 CAAGGGTTCAATGCACTTGT  20
                                    10        20


Chain D from PDB  Type:DNA  Length:20
                                                    
                 4umm D   1 GACAAGTGCATTGAACCCTT  20
                                    10        20


Chain E from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eee..eeehhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh..hhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4umm E 141 RQQEELCLVCGDRASGYHYNALTCEGCKGFFRRSVTKNAVYICKFGHACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKR 227
                                   150       160       170       180       190       200       210       220       


Chain F from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4umm F 205 VQELSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTERTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALR 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 G from PDB  Type:PROTEIN  Length:236
                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4umm G 287 VPPLTANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKNRKLPPFLEEIWDVA 529
                                   296       306       316      |333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523      
                                                              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  (0, 0)

(no "SCOP Domain" information available for 4UMM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UMM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UMM)

(-) Gene Ontology  (14, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ECR_HELVI | O18473: 1r1k 1r20 2r40
UniProtKB/TrEMBL
        Q7SIF6_HELVI | Q7SIF6: 1g2n 1r1k 1r20 2r40 3ixp

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