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(-) Description

Title :  SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A (SAP-1)/DNA COMPLEX
 
Authors :  Y. Mo, B. Vaessen, K. Johnston, R. Marmorstein
Date :  05 May 98  (Deposition) - 21 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ets Domain, Dna-Binding Domain, Winged Helix-Turn-Helix, Crystal Structure, Dna-Binding Specificity, Complex (Dna- Binding Protein/Dna), Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Mo, B. Vaessen, K. Johnston, R. Marmorstein
Structures Of Sap-1 Bound To Dna Targets From The E74 And C-Fos Promoters: Insights Into Dna Sequence Discrimination By Ets Proteins.
Mol. Cell V. 2 201 1998
PubMed-ID: 9734357  |  Reference-DOI: 10.1016/S1097-2765(00)80130-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*AP*CP*AP*GP*GP*AP*TP*GP*TP*G)-3')
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*CP*AP*CP*AP*TP*CP*CP*TP*GP*TP*C)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - PROTEIN (ETS-DOMAIN PROTEIN)
    Cellular Location: NUCLEUS
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: SAP-1 RESIDUES 1-93
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Variant: LYSS
    Expression System Vector: PRSETA
    Expression System Vector Type: BACTERIA
    Fragment: ETS DOMAIN, RESIDUES 1-93
    Gene: SAP-1 RESIDUES 1-93
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SAP-1, SERUM RESPONSE FACTOR ACCESSORY PROTEIN 1A, ELK4, SRF ACCESSORY PROTEIN 1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1BC7)

(-) Sites  (0, 0)

(no "Site" information available for 1BC7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BC7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr C:87 -Pro C:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BC7)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.ELK4_HUMAN5-85  1C:5-85
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.ELK4_HUMAN7-15  1C:7-15
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.ELK4_HUMAN51-66  1C:51-66

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003579921ENSE00001235111chr1:205601090-205600760331ELK4_HUMAN-00--
1.3ENST000003579923ENSE00002196582chr1:205593019-205592804216ELK4_HUMAN1-69691C:1-6969
1.4bENST000003579924bENSE00001372313chr1:205589966-205589094873ELK4_HUMAN70-3602911C:70-9324
1.5ENST000003579925ENSE00001040443chr1:205588201-205588085117ELK4_HUMAN361-399390--
1.6ENST000003579926ENSE00001416662chr1:205585772-2055770718702ELK4_HUMAN400-431320--

(-) 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:DNA  Length:11
                                          
                  1bc7 A  1 GACAGGATGTG 11
                                    10 


Chain B from PDB  Type:DNA  Length:11
                                          
                  1bc7 B 12 CACATCCTGTC 22
                                    21 


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with ELK4_HUMAN | P28324 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
            ELK4_HUMAN    1 MDSAITLWQFLLQLLQKPQNKHMICWTSNDGQFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILNM 93
               SCOP domains d1bc7c_ C: Serum response factor accessory protein 1a, SAP-1                                  SCOP domains
               CATH domains 1bc7C00 C:1-93 'winged helix' repressor DNA binding domain                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..eee.....eeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eee......eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ETS_DOMAIN_3  PDB: C:5-85 UniProt: 5-85                                          -------- PROSITE (1)
                PROSITE (2) ------ETS_DOMAI-----------------------------------ETS_DOMAIN_2    --------------------------- PROSITE (2)
               Transcript 1 Exon 1.3  PDB: C:1-69 UniProt: 1-69                                  Exon 1.4b  PDB: C:70-93  Transcript 1
                  1bc7 C  1 MDSAITLWQFLLQLLQKPQNKHMICWTSNDGQFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILNM 93
                                    10        20        30        40        50        60        70        80        90
   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)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BC7)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (ELK4_HUMAN | P28324)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    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: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:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory 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.
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0070932    histone H3 deacetylation    The modification of histone H3 by the removal of one or more acetyl groups.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces 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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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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    Tyr C:87 - Pro C:88   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        ELK4_HUMAN | P28324: 1bc8 1hbx 1k6o

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