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(-) Description

Title :  CRYSTAL STRUCTURE OF A SPT6-IWS1(SPN1) COMPLEX FROM ENCEPHALITOZOON CUNICULI, FORM III
 
Authors :  M. -L. Diebold, M. Koch, V. Cura, J. Cavarelli, C. Romier
Date :  27 Aug 10  (Deposition) - 17 Nov 10  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.74
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Elongation, Histone Chaperone, Rna Polymerase Ii, Mrna Export (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. -L. Diebold, M. Koch, E. Loeliger, V. Cura, F. Winston, J. Cavarelli C. Romier
The Structure Of An Iws1/Spt6 Complex Reveals An Interaction Domain Conserved In Tfiis, Elongin A And Med26
Embo J. V. 29 3979 2010
PubMed-ID: 21057455  |  Reference-DOI: 10.1038/EMBOJ.2010.272

(-) Compounds

Molecule 1 - IWS1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-MCN
    Fragment: EVOLUTIONARY CONSERVED DOMAIN, RESIDUES 55-198
    Organism Scientific: ENCEPHALITOZOON CUNICULI
    Organism Taxid: 6035
    Synonym: ECU08_0440
 
Molecule 2 - CHROMATIN STRUCTURE MODULATOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNEA-TH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-MCN
    Fragment: N-TERMINAL FRAGMENT, RESIDUES 34-71
    Organism Scientific: ENCEPHALITOZOON CUNICULI
    Organism Taxid: 6035
    Synonym: SPT6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2XPP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XPP)

(-) 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:137
 aligned with Q8SUS7_ENCCU | Q8SUS7 from UniProtKB/TrEMBL  Length:183

    Alignment length:137
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       
         Q8SUS7_ENCCU    42 GTVLEISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVFK 178
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------Med26-2xppA01 A:154-193                  Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpp A  57 GTVLEISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVFK 193
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       


Chain B from PDB  Type:PROTEIN  Length:24
 aligned with Q8SRG7_ENCCU | Q8SRG7 from UniProtKB/TrEMBL  Length:894

    Alignment length:24
                                    53        63    
         Q8SRG7_ENCCU    44 IDYGDRDSLFFEIFGTGEEYRYVL  67
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
                 Transcript ------------------------ Transcript
                 2xpp B  44 IDYGDRDSLFFEIFGTGEEYRYVL  67
                                    53        63
   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  (0, 0)

(no "SCOP Domain" information available for 2XPP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Med26] (7)

(-) Gene Ontology  (18, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8SUS7_ENCCU | Q8SUS7)
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:0001076    transcription factor 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 modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
    GO:0000991    transcription factor activity, core RNA polymerase II binding    Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. 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:0034401    chromatin organization involved in regulation of transcription    Any cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin that modulates the rate, frequency or extent of DNA-dependent transcription.
    GO:0030702    chromatin silencing at centromere    Repression of transcription of centromeric DNA by altering the structure of chromatin.
    GO:0006348    chromatin silencing at telomere    Repression of transcription of telomeric DNA by altering the structure of chromatin.
    GO:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0034243    regulation of transcription elongation from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    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: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:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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 B   (Q8SRG7_ENCCU | Q8SRG7)
molecular function
    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).
biological process
    GO:0032784    regulation of DNA-templated transcription, elongation    Any process that modulates the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides catalyzed by a DNA-dependent RNA polymerase.
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8SRG7_ENCCU | Q8SRG7: 2xpn 2xpo
        Q8SUS7_ENCCU | Q8SUS7: 2xpl 2xpn 2xpo

(-) Related Entries Specified in the PDB File

2xpl CRYSTAL STRUCTURE OF IWS1(SPN1) CONSERVED DOMAIN FROM ENCEPHALITOZOON CUNICULI
2xpn CRYSTAL STRUCTURE OF A SPT6-IWS1(SPN1) COMPLEX FROM ENCEPHALITOZOON CUNICULI, FORM I
2xpo CRYSTAL STRUCTURE OF A SPT6-IWS1(SPN1) COMPLEX FROM ENCEPHALITOZOON CUNICULI, FORM II