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(-) Description

Title :  DNA BINDING DOMAIN OF EARLY B-CELL FACTOR 1 (EBF1) BOUND TO DNA (CRYSTAL FORM I)
 
Authors :  N. Treiber, T. Treiber, G. Zocher, R. Grosschedl
Date :  17 Apr 10  (Deposition) - 01 Dec 10  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription Factor, Pseudo-Ig-Fold, Zn-Finger, Zn-Knuckle, Dna, Transcription-Dna Complex, Ebf, Ebf-1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Treiber, T. Treiber, G. Zocher, R. Grosschedl
Structure Of An Ebf1:Dna Complex Reveals Unusual Dna Recognition And Structural Homology With Rel Proteins
Genes Dev. V. 24 2270 2010
PubMed-ID: 20876732  |  Reference-DOI: 10.1101/GAD.1976610

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR COE1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23D
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA BINDING DOMAIN
    Gene: EBF1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: EBF1, O/E-1, OE-1, EARLY B-CELL FACTOR
 
Molecule 2 - DNA (5'- D(*CP*TP*TP*TP*AP*TP*TP*CP*CP*CP*AP*TP*GP*GP*GP*AP*AP*TP*AP*AP*AP*G)- 3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: SYNTHETIC OLIGONUCLEOTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:157 , CYS A:161 , CYS A:164 , CYS A:170BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREHIS B:157 , CYS B:161 , CYS B:164 , CYS B:170BINDING SITE FOR RESIDUE ZN B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COEPS01345 COE family signature.COE1_MOUSE161-170
 		  2A:161-170
B:161-170

(-) Exons   (0, 0)

(no "Exon" information available for 3MLO)

(-) 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:212
 aligned with COE1_MOUSE | Q07802 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:261
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294 
           COE1_MOUSE    35 GVLDANTAAQSGVGLARAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVGFVEKEKEANSEKTNNGIHYRLQLLYSNGIRTEQDFYVRLIDSMTKQAIVYEGQDKNPEMCRVLLTHEIMCSRCCDKKSCGNRNETPSDPVIIDRFFLKFFLKCNQNCLKNAGNPRDMRRFQVVVSTTVNVDGHVLAVSDNMFVHNNSKHGRRARRLDPSEGTPSYLEHATPCIKAISPSEGWTTGGATVIIIGDNFFDGLQVIF 295
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhh.....eeeeee....eee...eeeeeeeee.....eeeeeeeeeeee.hhhhhhhhh.....eeeeeeee.....eeeeeeeeeeee..............hhhhh..ee.....hhhhhh...hhhhhhh....eee...eeeeeeee................eeeeee........eeeeeeeeeee......-------------------------------------------....------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------COE       ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mlo A  35 GVLDANTAAQSGVGLARAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVGFVEKEKEANSEKTNNGIHYRLQLLYSNGIRTEQDFYVRLIDSMTKQAIVYEGQDKNPEMCRVLLTHEIMCSRCCDKKSCGNRNETPSDPVIIDRFFLKFFLKCNQNCLKNAGNPRDMRRFQVVVSTTVNVDGHVLAVSDNMFVHNNSKHG-------------------------------------------ENLY------F 246
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      |  -         -         -         -         -|  |     -|
                                                                                                                                                                                                                                        241                                         242  |    246
                                                                                                                                                                                                                                                                                       245       


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with COE1_MOUSE | Q07802 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:224
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254    
           COE1_MOUSE    35 GVLDANTAAQSGVGLARAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVGFVEKEKEANSEKTNNGIHYRLQLLYSNGIRTEQDFYVRLIDSMTKQAIVYEGQDKNPEMCRVLLTHEIMCSRCCDKKSCGNRNETPSDPVIIDRFFLKFFLKCNQNCLKNAGNPRDMRRFQVVVSTTVNVDGHVLAVSDNMFVHNNSKHGRRARRLDPSEGTPSYLE 258
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..........eeeeeeee....eee...eeeeeeeeee......eeee..eeee.hhhhhhhhh.....eeeeeeee.....eeeeeeeeeeee..............hhhhh..ee..............hhhhhhh....eee...eeeeeeee................eeeeee..........ee....eee......-----------...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------COE       ---------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mlo B  35 GVLDANTAAQSGVGLARAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVGFVEKEKEANSEKTNNGIHYRLQLLYSNGIRTEQDFYVRLIDSMTKQAIVYEGQDKNPEMCRVLLTHEIMCSRCCDKKSCGNRNETPSDPVIIDRFFLKFFLKCNQNCLKNAGNPRDMRRFQVVVSTTVNVDGHVLAVSDNMFVHNNSKHG-----------ENLYFQ 247
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      |  -       243    
                                                                                                                                                                                                                                        241         242     


Chain C from PDB  Type:DNA  Length:22
                                                      
                 3mlo C   1 CTTTATTCCCATGGGAATAAAG  22
                                    10        20  


Chain D from PDB  Type:DNA  Length:22
                                                      
                 3mlo D   1 CTTTATTCCCATGGGAATAAAG  22
                                    10        20
   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 3MLO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (COE1_MOUSE | Q07802)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for 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: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:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
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: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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        COE1_MOUSE | Q07802: 3mln 3mlp

(-) Related Entries Specified in the PDB File

3mln 3mlp