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(-) Description

Title :  CRYSTAL STRUCTURE OF CSL BOUND TO DNA
 
Authors :  R. A. Kovall, W. A. Hendrickson
Date :  23 Jun 04  (Deposition) - 31 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Beta-Trefoil Domain, Protein-Dna Complex, Rel Homology Region, Csl, Notch Signaling, Transcription Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Kovall, W. A. Hendrickson
Crystal Structure Of The Nuclear Effector Of Notch Signaling, Csl, Bound To Dna
Embo J. V. 23 3441 2004
PubMed-ID: 15297877  |  Reference-DOI: 10.1038/SJ.EMBOJ.7600349
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(*TP*TP*AP*CP*TP*GP*TP*GP*GP*GP*AP*AP*AP*GP*A)-3'
    Chains: B
    Engineered: YES
    Other Details: THE SEQUENCE COMES FROM A REGION WITHIN THE MAMMALIAN HES-1 PROMOTER
    Synthetic: YES
 
Molecule 2 - 5'- D(*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*AP*CP*AP*GP*T)-3'
    Chains: C
    Engineered: YES
    Other Details: THE SEQUENCE COMES FROM A REGION WITHIN THE MAMMALIAN HES-1 PROMOTER
    Synthetic: YES
 
Molecule 3 - LIN-12 AND GLP-1 TRANSCRIPTIONAL REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P-1
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CONSERVED CORE (RESIDUES 192-663)
    Gene: LAG-1
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
    Synonym: CLS

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric/Biological Unit (1, 9)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:220 , TYR A:243 , ILE A:245BINDING SITE FOR RESIDUE EDO A 51
2AC2SOFTWAREPRO A:639 , ILE A:640 , SER A:641 , SER A:651 , SER A:652 , GLY A:653 , LEU A:654BINDING SITE FOR RESIDUE EDO A 52
3AC3SOFTWARECYS A:241 , TYR A:243 , TRP A:422 , VAL A:461BINDING SITE FOR RESIDUE EDO A 53
4AC4SOFTWAREEDO A:55 , ALA A:544 , GLU A:545BINDING SITE FOR RESIDUE EDO A 54
5AC5SOFTWAREEDO A:54 , ARG A:584BINDING SITE FOR RESIDUE EDO A 55
6AC6SOFTWAREEDO A:58 , VAL A:224 , GLN A:226 , PHE A:236 , CYS A:237BINDING SITE FOR RESIDUE EDO A 56
7AC7SOFTWAREPHE A:395 , ASN A:396 , ARG A:397 , LYS A:495 , ALA A:535 , THR A:537 , DG B:8BINDING SITE FOR RESIDUE EDO A 57
8AC8SOFTWAREEDO A:56 , GLN A:226 , ARG A:234 , PHE A:235 , DT B:7BINDING SITE FOR RESIDUE EDO A 58

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:237 -Pro A:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TTU)

(-) 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:435
 aligned with Q8MXE7_CAEEL | Q8MXE7 from UniProtKB/TrEMBL  Length:671

    Alignment length:466
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652      
         Q8MXE7_CAEEL   193 VQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKLKKDRVAQLYKTLKASAQKDAAIENDPIHEQQATELVAYIGIGSDTSERQQLDFSTGKVRHPGDQRQDPNIYDYCAAKTLYISDSDKRKYFDLNAQFFYGCGMEIGGFVSQRIKVISKPSKKKQSMKNTDCKYLCIASGTKVALFNRLRSQTVSTRYLHVEGNAFHASSTKWGAFTIHLFDDERGLQETDNFAVRDGFVYYGSVVKLVDSVTGIALPRLRIRKVDKQQVILDASCSEEPVSQLHKCAFQMIDNELVYLCLSHDKIIQHQATAINEHRHQINDGAAWTIISTDKAEYRFFEAMGQVANPISPCPVVGSLEVDGHGEASRVELHGRDFKPNLKVWFGATPVETTFRSEESLHCSIPPVSQVRNEQTHWMFTNRTTGDVEVPISLVRDDGVVYSSGLTFSYKS 658
               SCOP domains -d1ttua2 A:196-380 DNA-binding protein LAG-1 (CSL)                                                                                                                                        d1ttua3 A:381-541 DNA-binding protein LAG-1 (CSL)                                                                                                                d1ttua1 A:542-660 DNA-binding protein LAG-1 (CSL)                                                                       SCOP domains
               CATH domains 1ttuA01 A:195-376,A:541-562 Lin-12 and glp-1 transcriptional regulat                 or; domain 1                                                                                     1ttuA02 A:377-540  [code=2.80.10.50, no name defined]                                                                                                               1ttuA01               1ttuA03 A:563-660 Immunoglobulins                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhheeeeeeee.eee..............eeeee.hhhhhhhhhhhhhhh.-----------------......eeeeeee.......eee..--------------..eeeeee.............ee.eeeeeee....eeeeee...eeee.............hhhhhh.....eeeeee....hhhhheeeeee..eeeee......eeeee........................eeeeee.........eeeeeee..ee....hhhhh......eeeee.........eee..eee..............hhhhheeeeeeeeeeeeeee.............eeeeeeee.hhhh.eeeeeee.....eeeee..ee..eeeee..eeeee..hhhhhhhhhhhh..........eeeeeeee...eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ttu A 195 VQSLTSDRMIDFLSNKEKYECVISIFHAKVAQKSYGNEKRFFCPPPCIYLIGQGWKLKKDRVAQLYKT-----------------EQQATELVAYIGIGSDTSERQQLDF--------------PNIYDYCAAKTLYISDSDKRKYFDLNAQFFYGCGMEIGGFVSQRIKVISKPSKKKQSMKNTDCKYLCIASGTKVALFNRLRSQTVSTRYLHVEGNAFHASSTKWGAFTIHLFDDERGLQETDNFAVRDGFVYYGSVVKLVDSVTGIALPRLRIRKVDKQQVILDASCSEEPVSQLHKCAFQMIDNELVYLCLSHDKIIQHQATAINEHRHQINDGAAWTIISTDKAEYRFFEAMGQVANPISPCPVVGSLEVDGHGEASRVELHGRDFKPNLKVWFGATPVETTFRSEESLHCSIPPVSQVRNEQTHWMFTNRTTGDVEVPISLVRDDGVVYSSGLTFSYKS 660
                                   204       214       224       234       244       254       | -         -     | 284       294       304         -    |  324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654      
                                                                                             262               280                     304            319                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:DNA  Length:15
                                               
                 1ttu B   1 TTACTGTGGGAAAGA  15
                                    10     


Chain C from PDB  Type:DNA  Length:15
                                               
                 1ttu C   1 AATCTTTCCCACAGT  15
                                    10
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8MXE7_CAEEL | Q8MXE7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005112    Notch binding    Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
    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: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.
biological process
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0001708    cell fate specification    The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
    GO:0043054    dauer exit    Exit from the facultative diapause of the dauer (enduring) larval stage of nematode development.
    GO:0042078    germ-line stem cell division    The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes.
    GO:0002119    nematode larval development    The process whose specific outcome is the progression of the nematode larva over time, from its formation to the mature structure. Nematode larval development begins with the newly hatched first-stage larva (L1) and ends with the end of the last larval stage (for example the fourth larval stage (L4) in C. elegans). Each stage of nematode larval development is characterized by proliferation of specific cell lineages and an increase in body size without alteration of the basic body plan. Nematode larval stages are separated by molts in which each stage-specific exoskeleton, or cuticle, is shed and replaced anew.
    GO:0018991    oviposition    The deposition of eggs (either fertilized or not) upon a surface or into a medium such as water.
    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:0040026    positive regulation of vulval development    Any process that activates or increases the frequency, rate or extent of development of the vulva. Vulval development is the process whose specific outcome is the progression of the egg-laying organ of female and hermaphrodite nematodes over time, from its formation to the mature structure. In nematodes, the vulva is formed from ventral epidermal cells during larval stages to give rise to a fully formed vulva in the adult.
    GO:0042659    regulation of cell fate specification    Any process that mediates the adoption of a specific fate by a cell.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
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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        Q8MXE7_CAEEL | Q8MXE7: 2fo1 3brd

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