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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ETS1 DIMER DNA COMPLEX.
 
Authors :  E. P. Lamber, G. S. Kachalova, M. Wilmanns
Date :  24 Oct 06  (Deposition) - 04 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.58
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ets-1, Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. P. Lamber, L. Vanhille, L. C. Textor, G. S. Kachalova, M. H. Sieweke, M. Wilmanns
Regulation Of The Transcription Factor Ets-1 By Dna-Mediated Homo-Dimerization.
Embo J. V. 27 2006 2008
PubMed-ID: 18566588  |  Reference-DOI: 10.1038/EMBOJ.2008.117
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*T*AP*GP*AP*CP*AP*GP*GP*AP*AP*GP*CP*AP*CP*TP*TP*CP*CP*TP* GP*GP*AP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'- D(*A*CP*TP*CP*CP*AP*GP*GP*AP*AP*GP*TP*GP*CP*TP*TP*CP*CP*TP* GP*TP*CP*T)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - C-ETS-1 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM10
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 280-441
    Gene: ETS1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: P54

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2NNY)

(-) Sites  (0, 0)

(no "Site" information available for 2NNY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NNY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NNY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NNY)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.ETS1_HUMAN335-415
 		  2A:335-415
B:335-415
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.ETS1_HUMAN337-345
 		  2A:337-345
B:337-345
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.ETS1_HUMAN381-396
 		  2A:381-396
B:381-396

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.6bENST000003193976bENSE00002154831chr11:128392199-128391808392ETS1_HUMAN1-28280--
1.7ENST000003193977ENSE00000917328chr11:128360471-128360352120ETS1_HUMAN28-68410--
1.8ENST000003193978ENSE00000917327chr11:128359385-128359185201ETS1_HUMAN68-135680--
1.9ENST000003193979ENSE00000917326chr11:128356041-12835596478ETS1_HUMAN135-161270--
1.10aENST0000031939710aENSE00000917325chr11:128354966-128354718249ETS1_HUMAN161-244840--
1.11bENST0000031939711bENSE00000917324chr11:128350346-128350086261ETS1_HUMAN244-331882A:308-331
B:308-331		24
24
1.12bENST0000031939712bENSE00000917323chr11:128333522-128333404119ETS1_HUMAN331-370402A:331-370
B:331-370		40
40
1.13cENST0000031939713cENSE00002159982chr11:128332471-128331745727ETS1_HUMAN371-441712A:371-436
B:371-436		66
66

(-) 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:129
 aligned with ETS1_HUMAN | P14921 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:129
                                   317       327       337       347       357       367       377       387       397       407       417       427         
           ETS1_HUMAN   308 VRDRADLNKDKPVIPAAALAGYTGSGPIQLWQFLLELLTDKSCQSFISWTGDGWEFKLSDPDEVARRWGKRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQSLLGYTPEELHAMLDVK 436
               SCOP domains d2nnya_ A: automated matches                                                                                                      SCOP domains
               CATH domains 2nnyA00 A:308-436 'winged helix' repressor DNA binding domain                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhhh....hhhhhhhhhhhhhhhhhh.ee.....eee..hhhhhhhhhhhhhh....hhhhhhhhhhhhhh...eee......eeee..hhhhhhh.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------ETS_DOMAIN_3  PDB: A:335-415 UniProt: 335-415                                    --------------------- PROSITE (1)
                PROSITE (2) -----------------------------ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.11b [INCOMPLETE] ---------------------------------------Exon 1.13c  PDB: A:371-436 UniProt: 371-441 [INCOMPLETE]           Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.12b  PDB: A:331-370              ------------------------------------------------------------------ Transcript 1 (2)
                 2nny A 308 VRDRADLNKDKPVIPAAALAGYTGSGPIQLWQFLLELLTDKSSQSFISWTGDGWEFKLSDPDEVARRWGKRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVSDLQSLLGYTPEELHAMLDVK 436
                                   317       327       337       347       357       367       377       387       397       407       417       427         


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with ETS1_HUMAN | P14921 from UniProtKB/Swiss-Prot  Length:441

    Alignment length:129
                                   317       327       337       347       357       367       377       387       397       407       417       427         
           ETS1_HUMAN   308 VRDRADLNKDKPVIPAAALAGYTGSGPIQLWQFLLELLTDKSCQSFISWTGDGWEFKLSDPDEVARRWGKRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQSLLGYTPEELHAMLDVK 436
               SCOP domains d2nnyb_ B: automated matches                                                                                                      SCOP domains
               CATH domains 2nnyB00 B:308-436 'winged helix' repressor DNA binding domain                                                                     CATH domains
           Pfam domains (1) --------------------------Ets-2nnyB01 B:334-417                                                               ------------------- Pfam domains (1)
           Pfam domains (2) --------------------------Ets-2nnyB02 B:334-417                                                               ------------------- Pfam domains (2)
         Sec.struct. author ..............hhhhhhhhhh....hhhhhhhhhhhhhhhh..eee.....eeee.hhhhhhhhhhhhhh....hhhhhhhhhhh......eee......eeee...hhhhhh.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------ETS_DOMAIN_3  PDB: B:335-415 UniProt: 335-415                                    --------------------- PROSITE (1)
                PROSITE (2) -----------------------------ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.11b [INCOMPLETE] ---------------------------------------Exon 1.13c  PDB: B:371-436 UniProt: 371-441 [INCOMPLETE]           Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.12b  PDB: B:331-370              ------------------------------------------------------------------ Transcript 1 (2)
                 2nny B 308 VRDRADLNKDKPVIPAAALAGYTGSGPIQLWQFLLELLTDKSSQSFISWTGDGWEFKLSDPDEVARRWGKRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVSDLQSLLGYTPEELHAMLDVK 436
                                   317       327       337       347       357       367       377       387       397       407       417       427         


Chain C from PDB  Type:DNA  Length:22
                                                      
                 2nny C   2 AGACAGGAAGCACTTCCTGGAG  23
                                    11        21  


Chain D from PDB  Type:DNA  Length:22
                                                      
                 2nny D   2 CTCCAGGAAGTGCTTCCTGTCT  23
                                    11        21
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Family: Ets (14)
(-)
Homo sapiens (Human) (6)
1aEts-2nnyB01B:334-417
1bEts-2nnyB02B:334-417

(-) Gene Ontology  (51, 51)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ETS1_HUMAN | P14921)
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:0035035    histone acetyltransferase binding    Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0000982    transcription factor 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 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.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0030578    PML body organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of PML bodies, a class of nuclear body; they react against SP100 auto-antibodies (PML = promyelocytic leukemia).
    GO:0060055    angiogenesis involved in wound healing    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury.
    GO:0048870    cell motility    Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0044849    estrous cycle    A type of ovulation cycle, which occurs in most mammalian therian females, where the endometrium is resorbed if pregnancy does not occur.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0021854    hypothalamus development    The progression of the hypothalamus region of the forebrain, from its initial formation to its mature state.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0021983    pituitary gland development    The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0051272    positive regulation of cellular component movement    Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
    GO:0010595    positive regulation of endothelial cell migration    Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0045648    positive regulation of erythrocyte differentiation    Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:1904996    positive regulation of leukocyte adhesion to vascular endothelial cell    Any process that activates or increases the frequency, rate or extent of leukocyte adhesion to vascular endothelial 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:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0061614    pri-miRNA transcription from RNA polymerase II promoter    The cellular synthesis of primary microRNA (pri-miRNA) transcripts from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. pri-miRNA transcripts are subsequently processed to produce the ~22nt miRNAs that function in gene regulation.
    GO:0045765    regulation of angiogenesis    Any process that modulates the frequency, rate or extent of angiogenesis.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0010715    regulation of extracellular matrix disassembly    Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix.
    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:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0001666    response to hypoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0070555    response to interleukin-1    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-1 stimulus.
    GO:0034616    response to laminar fluid shear stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a laminar fluid shear stress stimulus. Laminar fluid flow is the force acting on an object in a system where the fluid is moving across a solid surface in parallel layers. As an example, laminar shear stress can be seen where blood flows against the luminal side of blood vessel walls.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    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: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.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ETS1_HUMAN | P14921: 1gvj 2stt 2stw 3mfk 3ri4 3wts 3wtt 3wtu 3wtv 3wtw 3wtx 3wty 3wtz 3wu0 3wu1 4l0y 4l0z 4l18 4lg0

(-) Related Entries Specified in the PDB File

1gvj 1k78