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(-) Description

Title :  CRYSTAL STRUCTURE OF A SPT6-IWS1(SPN1) COMPLEX FROM ENCEPHALITOZOON CUNICULI, FORM II
 
Authors :  M. -L. Diebold, M. Koch, V. Cura, D. Moras, J. Cavarelli, C. Romier
Date :  27 Aug 10  (Deposition) - 17 Nov 10  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C
    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, D
    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 53-71
    Organism Scientific: ENCEPHALITOZOON CUNICULI
    Organism Taxid: 6035
    Synonym: SPT6

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:132 , ASN A:133 , ILE A:136 , HOH A:2018 , HOH A:2022BINDING SITE FOR RESIDUE CL A 200
2AC2SOFTWARELYS C:90 , ASN C:133 , ILE C:136 , HOH C:2016 , HOH C:2018BINDING SITE FOR RESIDUE CL C 200

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XPO)

(-) Sequences/Alignments

Asymmetric 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:139
 aligned with Q8SUS7_ENCCU | Q8SUS7 from UniProtKB/TrEMBL  Length:183

    Alignment length:139
                                    48        58        68        78        88        98       108       118       128       138       148       158       168         
         Q8SUS7_ENCCU    39 LDPGTVLEISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVF 177
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpo A  54 MDPGTVLEISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVF 192
                                    63        73        83        93       103       113       123       133       143       153       163       173       183         


Chain B from PDB  Type:PROTEIN  Length:15
 aligned with Q8SRG7_ENCCU | Q8SRG7 from UniProtKB/TrEMBL  Length:894

    Alignment length:15
                                    62     
         Q8SRG7_ENCCU    53 FFEIFGTGEEYRYVL  67
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 2xpo B  53 FFEIFGTGEEYRYVL  67
                                    62     


Chain C from PDB  Type:PROTEIN  Length:139
 aligned with Q8SUS7_ENCCU | Q8SUS7 from UniProtKB/TrEMBL  Length:183

    Alignment length:139
                                    48        58        68        78        88        98       108       118       128       138       148       158       168         
         Q8SUS7_ENCCU    39 LDPGTVLEISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVF 177
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------Med26-2xpoC01 C:154-192                 Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------Med26-2xpoC02 C:154-192                 Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xpo C  54 MDPGTVLEISRSLKKRMQDILKKDNANNLEGRPATGKIENVEEISDILMSKALQESLLDEGILDEIKGWLEPLPDKSMPNIKIRKRLLDVLKTMKIHKEHLVTSGVGKIVYFYSINPKESKEVRASAKALVQKWTNEVF 192
                                    63        73        83        93       103       113       123       133       143       153       163       173       183         


Chain D from PDB  Type:PROTEIN  Length:14
 aligned with Q8SRG7_ENCCU | Q8SRG7 from UniProtKB/TrEMBL  Length:894

    Alignment length:14
                                    62    
         Q8SRG7_ENCCU    53 FFEIFGTGEEYRYV  66
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 2xpo D  53 FFEIFGTGEEYRYV  66
                                    62
   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 2XPO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (18, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (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,D   (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 2xpp
        Q8SUS7_ENCCU | Q8SUS7: 2xpl 2xpn 2xpp

(-) 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
2xpp CRYSTAL STRUCTURE OF A SPT6-IWS1(SPN1) COMPLEX FROM ENCEPHALITOZOON CUNICULI, FORM III