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(-) Description

Title :  ESTROGEN RELATED RECEPTOR 2 DNA BINDING DOMAIN IN COMPLEX WITH DNA
 
Authors :  M. D. Gearhart, S. M. A. Holmbeck, R. M. Evans, H. J. Dyson, P. E. Wright
Date :  05 May 02  (Deposition) - 22 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (20x)
Keywords :  Estrogen Related Receptor 2, Dna Binding Domain, Herr2, Hormone Nuclear Receptor, Hormone/Growth Factor Receptor/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Gearhart, S. M. A. Holmbeck, R. M. Evans, H. J. Dyson, P. E. Wright
Monomeric Complex Of Human Orphan Estrogen Related Receptor-2 With Dna: A Pseudo-Dimer Interface Mediates Extended Half-Site Recognition
J. Mol. Biol. V. 327 819 2003
PubMed-ID: 12654265  |  Reference-DOI: 10.1016/S0022-2836(03)00183-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STEROID HORMONE RECEPTOR ERR2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: HERR2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ERR-BETA, ESTROGEN RECEPTOR-LIKE 2, ESTROGEN- RELATED RECEPTOR,BETA
 
Molecule 2 - 5'-D(*GP*CP*TP*CP*AP*AP*GP*GP*TP*CP*AP*CP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*TP*GP*AP*CP*CP*TP*TP*GP*AP*GP*C)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:103 , CYS A:106 , CYS A:120 , CYS A:123BINDING SITE FOR RESIDUE ZN A 195
2AC2SOFTWARECYS A:139 , CYS A:145 , CYS A:155 , CYS A:158BINDING SITE FOR RESIDUE ZN A 196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LO1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LO1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_043503A110VERR2_HUMANDisease (DFNB35)121909110AA110V
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUCLEAR_REC_DBD_2PS51030 Nuclear hormone receptors DNA-binding domain profile.ERR2_HUMAN100-175  1A:100-175
2NUCLEAR_REC_DBD_1PS00031 Nuclear hormones receptors DNA-binding region signature.ERR2_HUMAN103-129  1A:103-129

(-) Exons   (0, 0)

(no "Exon" information available for 1LO1)

(-) Sequences/Alignments

NMR Structure
   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:90
 aligned with ERR2_HUMAN | O95718 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:90
                                   106       116       126       136       146       156       166       176       186
           ERR2_HUMAN    97 AIPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQKYK 186
               SCOP domains d1lo1a_ A: Steroid hormone receptor Err2 DNA-binding domain                                SCOP domains
               CATH domains 1lo1A00 A:97-186 Erythroid Transcription Factor GATA-1, subunit A                          CATH domains
               Pfam domains ----zf-C4-1lo1A01 A:101-170                                               ---------------- Pfam domains
         Sec.struct. author .....ee....ee..ee....eehhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh.hhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------V---------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---NUCLEAR_REC_DBD_2  PDB: A:100-175 UniProt: 100-175                          ----------- PROSITE (1)
                PROSITE (2) ------NUCLEAR_REC_DBD_1          --------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 1lo1 A  97 AIPKRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQKYK 186
                                   106       116       126       136       146       156       166       176       186


Chain B from PDB  Type:DNA  Length:13
                                             
                 1lo1 B   1 GCTCAAGGTCACG  13
                                    10   


Chain C from PDB  Type:DNA  Length:13
                                             
                 1lo1 C  14 CGTGACCTTGAGC  26
                                    23
   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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: zf-C4] (14)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (ERR2_HUMAN | O95718)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    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: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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0001892    embryonic placenta development    The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0030522    intracellular receptor signaling pathway    Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
    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: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: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: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.

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