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(-) Description

Title :  ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING SURFACE AFFECT DNA-RECOGNITION
 
Authors :  Y. Mo, B. Vaessen, K. Johnston, R. Marmorstein
Date :  19 Jan 00  (Deposition) - 17 Apr 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Ets-Domain, Dna-Binding Domain, Winged Helix-Turn-Helix, Crystal Structure, Dna-Binding Specificity, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Mo, B. Vaessen, K. Johnston, R. Marmorstein
Structure Of The Elk-1-Dna Complex Reveals How Dna-Distal Residues Affect Ets Domain Recognition Of Dna.
Nat. Struct. Biol. V. 7 292 2000
PubMed-ID: 10742173  |  Reference-DOI: 10.1038/74055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3')
    Chains: A, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3')
    Chains: B, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - ETS-DOMAIN PROTEIN ELK-1
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-94
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRANSFORMING PROTEIN ELK-1, ELK1, MEMBER OF ETS ONCOGENE FAMILY

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1DUX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ETS_DOMAIN_3PS50061 Ets-domain profile.ELK1_HUMAN5-86
 		  2C:5-86
F:5-86
2ETS_DOMAIN_1PS00345 Ets-domain signature 1.ELK1_HUMAN7-15
 		  2C:7-15
F:7-15
3ETS_DOMAIN_2PS00346 Ets-domain signature 2.ELK1_HUMAN52-67
 		  2C:52-67
F:52-67

(-) Exons   (2, 4)

Asymmetric/Biological Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003769831bENSE00001853539X:47509990-47509822169ELK1_HUMAN-00--
1.2ENST000003769832ENSE00001472335X:47509425-47509320106ELK1_HUMAN-00--
1.4ENST000003769834ENSE00002166264X:47500874-47500631244ELK1_HUMAN1-70702C:5-70
F:5-70		66
66
1.5bENST000003769835bENSE00000867046X:47498737-47498294444ELK1_HUMAN71-2181482C:71-90
F:71-90		20
20
1.6ENST000003769836ENSE00000867045X:47497581-47497150432ELK1_HUMAN219-3621440--
1.7aENST000003769837aENSE00000867044X:47496513-47496412102ELK1_HUMAN363-396340--
1.8bENST000003769838bENSE00001815637X:47496326-47495566761ELK1_HUMAN397-428320--

(-) 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:13
                                            
                  1dux A  1 TGACCGGAAGTGT 13
                                    10   


Chain B from PDB  Type:DNA  Length:13
                                            
                  1dux B  1 ACACTTCCGGTCA 13
                                    10   


Chain C from PDB  Type:PROTEIN  Length:86
 aligned with ELK1_HUMAN | P19419 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:86
                                    14        24        34        44        54        64        74        84      
            ELK1_HUMAN    5 VTLWQFLLQLLREQGNGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRALRYYYDKNIIRKVSGQKFVYKFVSYPE 90
               SCOP domains d1duxc_ C: Elk-1                                                                       SCOP domains
               CATH domains 1duxC00 C:5-90 'winged helix' repressor DNA binding domain                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......eeee....eee..hhhhhhhhhhhh......hhhhhhhhhhhhhhhh.eee......eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ETS_DOMAIN_3  PDB: C:5-86 UniProt: 5-86                                           ---- PROSITE (1)
                PROSITE (2) --ETS_DOMAI------------------------------------ETS_DOMAIN_2    ----------------------- PROSITE (2)
               Transcript 1 Exon 1.4  PDB: C:5-70 UniProt: 1-70 [INCOMPLETE]                  Exon 1.5b            Transcript 1
                  1dux C  5 VTLWQFLLQLLREQGNGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRALRYYYDKNIIRKVSGQKFVYKFVSYPE 90
                                    14        24        34        44        54        64        74        84      


Chain D from PDB  Type:DNA  Length:13
                                            
                  1dux D  1 TGACCGGAAGTGT 13
                                    10   


Chain E from PDB  Type:DNA  Length:13
                                            
                  1dux E  1 ACACTTCCGGTCA 13
                                    10   


Chain F from PDB  Type:PROTEIN  Length:86
 aligned with ELK1_HUMAN | P19419 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:86
                                    14        24        34        44        54        64        74        84      
            ELK1_HUMAN    5 VTLWQFLLQLLREQGNGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRALRYYYDKNIIRKVSGQKFVYKFVSYPE 90
               SCOP domains d1duxf_ F: Elk-1                                                                       SCOP domains
               CATH domains 1duxF00 F:5-90 'winged helix' repressor DNA binding domain                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......eeee....eee..hhhhhhhhhhhhh.....hhhhhhhhhhhhh....eee......eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ETS_DOMAIN_3  PDB: F:5-86 UniProt: 5-86                                           ---- PROSITE (1)
                PROSITE (2) --ETS_DOMAI------------------------------------ETS_DOMAIN_2    ----------------------- PROSITE (2)
               Transcript 1 Exon 1.4  PDB: F:5-70 UniProt: 1-70 [INCOMPLETE]                  Exon 1.5b            Transcript 1
                  1dux F  5 VTLWQFLLQLLREQGNGHIISWTSRDGGEFKLVDAEEVARLWGLRKNKTNMNYDKLSRALRYYYDKNIIRKVSGQKFVYKFVSYPE 90
                                    14        24        34        44        54        64        74        84
   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  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C,F   (ELK1_HUMAN | P19419)
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:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    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:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    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: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: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:0071480    cellular response to gamma radiation    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 gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0071396    cellular response to lipid    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 lipid stimulus.
    GO:0071394    cellular response to testosterone stimulus    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 testosterone stimulus.
    GO:1901216    positive regulation of neuron death    Any process that activates or increases the frequency, rate or extent of neuron death.
    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:0071774    response to fibroblast growth factor    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 fibroblast growth factor stimulus.
    GO:0009416    response to light 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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    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:0043679    axon terminus    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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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