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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PEPTIDE BOUND COMPLEX OF THE ANKYRIN REPEAT DOMAINS OF HUMAN RFXANK
 
Authors :  R. Lam, C. Xu, C. B. Bian, J. Kania, C. Bountra, J. Weigelt, C. H. Arrowsmi A. M. Edwards, A. Bochkarev, J. Min, Structural Genomics Consortiu
Date :  12 Dec 11  (Deposition) - 04 Apr 12  (Release) - 13 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics Consortium, Sgc, Rfxank, Ank Repeat, Protein Binding, Rfx5 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Xu, J. Jin, C. Bian, R. Lam, R. Tian, R. Weist, L. You, J. Nie, A. Bochkarev, W. Tempel, C. S. Tan, G. A. Wasney, M. Vedadi, G. D. Gish, C. H. Arrowsmith, T. Pawson, X. J. Yang, J. Min
Sequence-Specific Recognition Of A Pxlpxi/L Motif By An Ankyrin Repeat Tumbler Lock.
Sci. Signal. V. 5 Ra39 2012
PubMed-ID: 22649097  |  Reference-DOI: 10.1126/SCISIGNAL.2002979

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN RFXANK
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-MHL
    Expression System StrainBL21-(DE3)-V2R-PRARE2
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 90-260 (ANK REPEATS)
    GeneANKRA1, RFXANK, RFXB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANKYRIN REPEAT FAMILY A PROTEIN 1, REGULATORY FACTOR X SUBUNIT B, RFX-B, REGULATORY FACTOR X-ASSOCIATED ANKYRIN-CONTAINING PROTEIN
 
Molecule 2 - DNA-BINDING PROTEIN RFX5
    ChainsB
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMAN RFX5.
    SynonymREGULATORY FACTOR X 5
    SyntheticYES

 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 3V30)

(-) Sites  (0, 0)

(no "Site" information available for 3V30)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V30)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V30)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009941L195PRFXK_HUMANDisease (BLS2)751386365AL195P
2UniProtVAR_014472Q251ERFXK_HUMANPolymorphism1802498AQ251E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REPEATPS50088 Ankyrin repeat profile.RFXK_HUMAN123-155
156-188
189-221
  3A:123-155
A:156-188
A:189-221

(-) Exons   (0, 0)

(no "Exon" information available for 3V30)

(-) 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:161
 aligned with RFXK_HUMAN | O14593 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:161
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           RFXK_HUMAN    92 LSIHQLAAQGELDQLKEHLRKGDNLVNKPDERGFTPLIWASAFGEIETVRFLLEWGADPHILAKERESALSLASTGGYTDIVGLLLERDVDINIYDWNGGTPLLYAVRGNHVKCVEALLARGADLTTEADSGYTPMDLAVALGYRKVQQVIENHILKLFQS 252
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhhhhhh..hhhhhh......hhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhh.hhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------P-------------------------------------------------------E- SAPs(SNPs)
                    PROSITE -------------------------------ANK_REPEAT  PDB: A:123-155       ANK_REPEAT  PDB: A:156-188       ANK_REPEAT  PDB: A:189-221       ------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v30 A  92 LSIHQLAAQGELDQLKEHLRKGDNLVNKPDERGFTPLIWASAFGEIETVRFLLEWGADPHILAKERESALSLASTGGYTDIVGLLLERDVDINIYDWNGGTPLLYAVRGNHVKCVEALLARGADLTTEADSGYTPMDLAVALGYRKVQQVIENHILKLFQS 252
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 

Chain B from PDB  Type:PROTEIN  Length:16
 aligned with RFX5_HUMAN | P48382 from UniProtKB/Swiss-Prot  Length:616

    Alignment length:16
                                   177      
           RFX5_HUMAN   168 TLVSMPPLPGLDLKGS 183
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ................ Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 3v30 B   2 TLVSMPPLPGLDLKGS  17
                                    11      

   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 3V30)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V30)

(-) Gene Ontology  (16, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RFXK_HUMAN | O14593)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    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:0007265    Ras protein signal transduction    A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
    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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0045171    intercellular bridge    A direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised.
    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.

Chain B   (RFX5_HUMAN | P48382)
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: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: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:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        RFX5_HUMAN | P483822kw3
        RFXK_HUMAN | O145933uxg 4qqm

(-) Related Entries Specified in the PDB File

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