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(-) Description

Title :  SANT DOMAIN STRUCTURE OF XENOPUS REMODELING FACTOR ISWI
 
Authors :  J. R. Horton, X. Cheng
Date :  25 Oct 06  (Deposition) - 11 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sant Domain; Histone-Tail Binding Module; Chromatin Binding; Helix-Turn-Helix, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Horton, S. J. Elgar, S. I. Khan, X. Zhang, P. A. Wade, X. Cheng
Structure Of The Sant Domain From The Xenopus Chromatin Remodeling Factor Iswi
Proteins V. 67 1198 2007
PubMed-ID: 17377988  |  Reference-DOI: 10.1002/PROT.21352
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISWI PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SANT DOMAIN
    Gene: ISWI
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:61 , HOH B:183 , ALA B:853 , VAL B:856 , LYS B:859BINDING SITE FOR RESIDUE MG B 9050
2AC2SOFTWAREHOH A:221 , HOH A:222 , ALA A:853 , VAL A:856 , LYS A:859BINDING SITE FOR RESIDUE MG A 9220

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NOG)

(-) Exons   (0, 0)

(no "Exon" information available for 2NOG)

(-) 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:157
 aligned with Q6DFM0_XENLA | Q6DFM0 from UniProtKB/TrEMBL  Length:1046

    Alignment length:157
                                   758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       
         Q6DFM0_XENLA   749 EPKVPKAPRPPKQPNVQDFQFFPPRLFELLEKEILYYRKTIGYKVPRNPDLPNSAQVQKEEQLKIDEAESLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQDIEKTMAQIERGEARIQ 905
               SCOP domains d2noga1 A:739-827 automated matches                                                     --------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhh.hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nog A 739 EPKVPKAPRPPKQPNVQDFQFFPPRLFELLEKEILYYRKTIGYKVPRNPDLPNSAQVQKEEQLKIDEAEPLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQDIEKTMAQIERGEARIQ 896
                                   748       758       768       778       788       799       809       819       829       839       849       859       869       879       889       
                                                                                   796|                                                                                                  
                                                                                    798                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with Q6DFM0_XENLA | Q6DFM0 from UniProtKB/TrEMBL  Length:1046

    Alignment length:156
                                   758       768       778       788       798       808       818       828       838       848       858       868       878       888       898      
         Q6DFM0_XENLA   749 EPKVPKAPRPPKQPNVQDFQFFPPRLFELLEKEILYYRKTIGYKVPRNPDLPNSAQVQKEEQLKIDEAESLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQDIEKTMAQIERGEARI 904
               SCOP domains d2nogb1 B:739-827 automated matches                                                     d2nogb2 B:828-895 automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) HAND-2nogB01 B:739-825                                                                -------------------------------------------------------SLIDE-2nogB03   Pfam domains (1)
           Pfam domains (2) HAND-2nogB02 B:739-825                                                                -------------------------------------------------------SLIDE-2nogB04   Pfam domains (2)
         Sec.struct. author ................hhhhh.hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nog B 739 EPKVPKAPRPPKQPNVQDFQFFPPRLFELLEKEILYYRKTIGYKVPRNPDLPNSAQVQKEEQLKIDEAEPLNDEELEEKEKLLTQGFTNWNKRDFNQFIKANEKWGRDDIENIAREVEGKTPEEVIEYSAVFWERCNELQDIEKTMAQIERGEARI 895
                                   748       758       768       778       788       799       809       819       829       839       849       859       869       879       889      
                                                                                   796|                                                                                                 
                                                                                    798
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NOG)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: HAND] (4)
(-)
Clan: no clan defined [family: SLIDE] (4)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6DFM0_XENLA | Q6DFM0)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0031491    nucleosome binding    Interacting selectively and non-covalently with a nucleosome, a complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
cellular component
    GO:0016589    NURF complex    An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.
    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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