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(-) Description

Title :  HUMAN EARLY B-CELL FACTOR 1 (EBF1) DNA-BINDING DOMAIN
 
Authors :  M. I. Siponen, M. Wisniewska, C. H. Arrowsmith, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Jo T. Karlberg, P. Kraulis, T. Kotenyova, N. Markova, M. Moche, P. Nordlu T. Nyman, C. Persson, H. Schuler, P. Schutz, L. Svensson, A. G. Thorsel L. Tresaugues, S. Van Den Berg, E. Wahlberg, J. Weigelt, M. Welin, H. Structural Genomics Consortium (Sgc)
Date :  28 Feb 10  (Deposition) - 16 Mar 10  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym./Biol. Unit :  A
Keywords :  Immunoglobulin (Ig)-Like Domain, Structural Genomics, Structural Genomics Consortium, Sgc, Activator, Developmental Protein, Dna- Binding, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc-Finger, Transcription Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. I. Siponen, M. Wisniewska, L. Lehtio, I. Johansson, L. Svensson, G. Raszewski, L. Nilsson, M. Sigvardsson, H. Berglund
Structural Determination Of Functional Domains In Early B-Cell Factor (Ebf) Family Of Transcription Factors Reveals Similarities To Rel Dna-Binding Proteins And A Novel Dimerization Motif.
J. Biol. Chem. V. 285 25875 2010
PubMed-ID: 20592035  |  Reference-DOI: 10.1074/JBC.C110.150482

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR COE1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3) R3 PRARE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDNA-BINDING DOMAIN
    GeneCOE1, EBF, EBF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymO/E-1, OE-1, EARLY B-CELL FACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
2NH41Ligand/IonAMMONIUM ION
3SO41Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:157 , CYS A:161 , CYS A:164 , CYS A:170BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREARG A:173 , PRO A:177 , SER A:178 , ASP A:179BINDING SITE FOR RESIDUE SO4 A 251
3AC3SOFTWAREARG A:163BINDING SITE FOR RESIDUE NH4 A 252

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1COEPS01345 COE family signature.COE1_HUMAN161-170  1A:161-170

(-) Exons   (0, 0)

(no "Exon" information available for 3LYR)

(-) 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:211
 aligned with COE1_HUMAN | Q9UH73 from UniProtKB/Swiss-Prot  Length:591

    Alignment length:217
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           COE1_HUMAN    21 GSGMNAVRTWMQGAGVLDANTAAQSGVGLARAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVGFVEKEKEANSEKTNNGIHYRLQLLYSNGIRTEQDFYVRLIDSMTKQAIVYEGQDKNPEMCRVLLTHEIMCSRCCDKKSCGNRNETPSDPVIIDRFFLKFFLKCNQNCLKNAGNPRDMRRFQVVVSTTVNVDGHVLAVSDNMFVHNN 237
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh....eehhhhhh....eeeeeeee....eee...eeeeeeeeee......eeeeeeeeee.hhhhhhhhh.....eeeeeeee.....eeeeeeeeeeee.....................ee.hhhhhhhhhh..............eee...eeeeeeee......------....eeeeee........eeee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------COE       ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lyr A  21 GSGmNAVRTWmQGAGVLDANTAAQSGVGLARAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVGFVEKEKEANSEKTNNGIHYRLQLLYSNGIRTEQDFYVRLIDSmTKQAIVYEGQDKNPEmCRVLLTHEImCSRCCDKKSCGNRNETPSDPVIIDRFFLKFFLKCNQNCLK------DmRRFQVVVSTTVNVDGHVLAVSDNmFVHNN 237
                               |    30|       40        50        60        70        80        90       100       110       120       130   |   140       150       160       170       180       190       200      |210       220       230 |     
                               |     31-MSE                                                                                                134-MSE         150-MSE   160-MSE                                 200    207|                     232-MSE 
                              24-MSE                                                                                                                                                                                 208-MSE                         

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  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 3LYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COE1_HUMAN | Q9UH73)
molecular function
    GO:0070742    C2H2 zinc finger domain binding    Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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: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: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_HUMAN | Q9UH733mqi

(-) Related Entries Specified in the PDB File

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