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(-) Description

Title :  CRYSTAL STRUCTURE OF YAN-SAM/MAE-SAM COMPLEX
 
Authors :  F. Qiao, H. Song, C. A. Kim, M. R. Sawaya, J. B. Hunter, M. Gingery, I. Rebay, A. J. Courey, J. U. Bowie
Date :  26 Mar 04  (Deposition) - 27 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Alpha-Helix, 3(10) Helix, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Qiao, H. Song, C. A. Kim, M. R. Sawaya, J. B. Hunter, M. Gingery, I. Rebay, A. J. Courey, J. U. Bowie
Derepression By Depolymerization; Structural Insights Into The Regulation Of Yan By Mae.
Cell(Cambridge, Mass. ) V. 118 163 2004
PubMed-ID: 15260987  |  Reference-DOI: 10.1016/J.CELL.2004.07.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ETS DNA-BINDING PROTEIN POKKURI
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET-3C
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SAM DOMAIN OF TRANSCRIPTION REPRESSOR YAN
    Gene: AOP, POK, YAN, CG3166
    Mutation: YES
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: PROTEIN YAN, PROTEIN ANTERIOR OPEN
 
Molecule 2 - MODULATOR OF THE ACTIVITY OF ETS CG15085-PA
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET-3C
    Expression System Strain: BL21-CODONPLUS(DE3)-RP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SAM DOMAIN OF TRANSCRIPTION REGULATOR MAE
    Gene: MAE
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1SV0)

(-) Sites  (0, 0)

(no "Site" information available for 1SV0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SV0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SV0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SV0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SV0)

(-) Exons   (0, 0)

(no "Exon" information available for 1SV0)

(-) Sequences/Alignments

Asymmetric 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:77
 aligned with POK_DROME | Q01842 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:77
                                    52        62        72        82        92       102       112       
            POK_DROME    43 LPPSLPSDPRLWSREDVLVFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHM 119
               SCOP domains d1sv0a_ A: Ets DNA-binding protein pokkuri (Yan)                              SCOP domains
               CATH domains 1sv0A00 A:43-119 Transcription Factor, Ets-1                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 1sv0 A  43 LPPSLPSDPRLWSREDVLVFLRFCVREFDLPKLDFDLFQMNGKRLCLLTRADFGHRCPGAGDVLHNVLQMLIIESHS 119
                                    52        62        72        82        92       102       112       


Chain B from PDB  Type:PROTEIN  Length:79
 aligned with POK_DROME | Q01842 from UniProtKB/Swiss-Prot  Length:732

    Alignment length:93
                                    51        61        71        81        91       101       111       121       131   
            POK_DROME    42 QLPPSLPSDPRLWSREDVLVFLRFCVREFDLPKLDFDLFQMNGKALCLLTRADFGHRCPGAGDVLHNVLQMLIIESHMMQWHLPNSPVTPTSR 134
               SCOP domains d1sv0b_ B: Ets DNA-binding protein pokkuri (Yan)                                              SCOP domains
               CATH domains 1sv0B00 B:42-120 Transcription Factor, Ets-1                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhh--------------h. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 1sv0 B  42 QLPPSLPSDPRLWSREDVLVFLRFCVREFDLPKLDFDLFQMNGKRLCLLTRADFGHRCPGAGDVLHNVLQMLIIESH--------------SR 120
                                    51        61        71        81        91       101       111      |  -         - | 
                                                                                                      118            119 


Chain C from PDB  Type:PROTEIN  Length:82
 aligned with Q7K119_DROME | Q7K119 from UniProtKB/TrEMBL  Length:177

    Alignment length:82
                                   103       113       123       133       143       153       163       173  
         Q7K119_DROME    94 PLGSDGLPLDPRDWTRADVWKWLINMAVSEGLEVTAELPQKFPMNGKALCLMSLDMYLCRVPVGGKMLYRDFRVRLARAMAL 175
               SCOP domains d1sv0c_ C: Modulator of the activity of Ets (MAE, CG15085-PA)                      SCOP domains
               CATH domains 1sv0C00 C:94-175 Transcription Factor, Ets-1                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1sv0 C  94 PLGSDGLPLDPRDWTRADVWKWLINMAVSEGLEVTAELPQKFPMNGKALCLMSLDMYLCRVPVGGKMLYRDFRVRLARAMSR 175
                                   103       113       123       133       143       153       163       173  


Chain D from PDB  Type:PROTEIN  Length:81
 aligned with Q7K119_DROME | Q7K119 from UniProtKB/TrEMBL  Length:177

    Alignment length:81
                                   104       114       124       134       144       154       164       174 
         Q7K119_DROME    95 LGSDGLPLDPRDWTRADVWKWLINMAVSEGLEVTAELPQKFPMNGKALCLMSLDMYLCRVPVGGKMLYRDFRVRLARAMAL 175
               SCOP domains d1sv0d_ D: Modulator of the activity of Ets (MAE, CG15085-PA)                     SCOP domains
               CATH domains 1sv0D00 D:95-175 Transcription Factor, Ets-1                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1sv0 D  95 LGSDGLPLDPRDWTRADVWKWLINMAVSEGLEVTAELPQKFPMNGKALCLMSLDMYLCRVPVGGKMLYRDFRVRLARAMSR 175
                                   104       114       124       134       144       154       164       174
   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  (2, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1SV0)

(-) Gene Ontology  (53, 59)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POK_DROME | Q01842)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    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:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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:0007254    JNK cascade    An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0007464    R3/R4 cell fate commitment    The process in which the R3/R4 photoreceptors commit to their cell fate. R3 and R4 are paired photoreceptors which contribute the outer rhabdomeres.
    GO:0045467    R7 cell development    The process whose specific outcome is the progression of the R7 photoreceptor over time, from its formation to the mature structure. The R7 photoreceptor is the last photoreceptor to develop in the ommatidium.
    GO:0007298    border follicle cell migration    The directed movement of a border cell through the nurse cells to reach the oocyte. An example of this is found in Drosophila melanogaster.
    GO:0001709    cell fate determination    A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment.
    GO:0048749    compound eye development    The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye.
    GO:0001751    compound eye photoreceptor cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0008340    determination of adult lifespan    The control of viability and duration in the adult phase of the life-cycle.
    GO:0007391    dorsal closure    The process during Drosophila embryogenesis whereby the ectodermal cells of the lateral epithelium stretch in a coordinated fashion to internalize the amnioserosa cells and close the embryo dorsally.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0008406    gonad development    The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones.
    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:0048747    muscle fiber development    The process whose specific outcome is the progression of the muscle fiber over time, from its formation to the mature structure. In skeletal muscle, fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0046580    negative regulation of Ras protein signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of Ras protein signal transduction.
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:0045596    negative regulation of cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation.
    GO:0045316    negative regulation of compound eye photoreceptor development    Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor development.
    GO:0035157    negative regulation of fusion cell fate specification    Any process that restricts, stops or prevents a cell from adopting a fusion cell fate. Once the terminal and fusion fates have been correctly induced, inhibitory feedback loops prevent the remaining branch cells from assuming similar fates.
    GO:0046533    negative regulation of photoreceptor cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster.
    GO:0035155    negative regulation of terminal cell fate specification, open tracheal system    Any process that restricts, stops or prevents a cell from adopting a terminal cell fate in an open tracheal system. Once the terminal and fusion fates have been correctly induced, inhibitory feedback loops prevent the remaining branch cells from assuming similar fates.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0060233    oenocyte delamination    The negative regulation of cell adhesion process in which an oenocyte splits off of an existing epithelial sheet.
    GO:0045678    positive regulation of R7 cell differentiation    Any process that activates or increases the frequency, rate or extent of R7 cell differentiation.
    GO:0090175    regulation of establishment of planar polarity    Any process that modulates the rate, frequency or extent of the establishment of planar polarity, the coordinated organization of groups of cells in a tissue, such that they all orient to similar coordinates.
    GO:0045610    regulation of hemocyte differentiation    Any process that modulates the frequency, rate or extent of hemocyte differentiation.
    GO:0050767    regulation of neurogenesis    Any process that modulates the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

Chain C,D   (Q7K119_DROME | Q7K119)
molecular function
    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: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:0001191    transcriptional repressor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0009880    embryonic pattern specification    The process that results in the patterns of cell differentiation that will arise in an embryo.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051168    nuclear export    The directed movement of substances out of the nucleus.
    GO:0042461    photoreceptor cell development    Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light.
    GO:0046578    regulation of Ras protein signal transduction    Any process that modulates the frequency, rate or extent of Ras protein signal transduction.
    GO:0042058    regulation of epidermal growth factor receptor signaling pathway    Any process that modulates the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
    GO:0042325    regulation of phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates 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:0007423    sensory organ development    The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure.
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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  1sv0
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  POK_DROME | Q01842
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  Q7K119_DROME | Q7K119
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 Related Entries

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

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        POK_DROME | Q01842: 1sv4

(-) Related Entries Specified in the PDB File

1sv4 CRYSTAL STRUCTURE OF YAN-SAM