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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE RIF2
 
Authors :  T. Shi, R. D. Bunker, H. Gut, A. Scrima, N. H. Thoma
Date :  15 Apr 13  (Deposition) - 19 Jun 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.94
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dna Binding Protein, Genome Stability, Telomere Associated Proteins, Aaa+ Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Shi, R. D. Bunker, S. Mattarocci, C. Ribeyre, M. Faty, H. Gut, A. Scrima, U. Rass, S. M. Rubin, D. Shore, N. H. Thoma
Rif1 And Rif2 Shape Telomere Funcation And Architecture Through Multivalent Rap1 Interactions
Cell(Cambridge, Mass. ) V. 153 1340 2013
PubMed-ID: 23746845  |  Reference-DOI: 10.1016/J.CELL.2013.05.007

(-) Compounds

Molecule 1 - PROTEIN RIF2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX BASED
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 65-380
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C
    Synonym: RAP1-INTERACTING FACTOR 2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:120 , HIS A:336 , PHE A:338BINDING SITE FOR RESIDUE CL A1374

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BJ1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:371 -Pro A:372

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4BJ1)

(-) 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:261
 aligned with RIF2_YEAST | Q06208 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:306
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367      
           RIF2_YEAST    68 HVFYQKFKSMALQELGTNYLSISYVPSLSKFLSKNLRSMKNCIVFFDKVEHIHQYAGIDRAVSETLSLVDINVVIIEMNDYLMKEGIQSSKSKECIESMGQASYSGQLDFEASEKPSNHTSDLMMMVMRKINNDESIDHIVYFKFEQLDKLSTSTIIEPSKLTEFINVLSVLEKSNNIAFKVLIYSNNVSISSLLSTSLKKKLNTKYTVFEMPILTCAQEQEYLKKMIKFTFDSGSKLLQSYNSLVTCQLNNKESNLAIFFEFLKVFPHPFTYLFNAYTEIIVQSRTFDELLDKIRNRLTIKNYPH 373
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhhh..eeeeeehhhhhh.-----------------------------------.hhhhhhhhhhhh......eeeeeeeee...------.hhhhhhhhhhhhhhhhhh..eeeeeeeee.----hhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bj1 A  68 HVFYQKFKSMALQELGTNYLSISYVPSLSKFLSKNLRSMKNCIVFFDKVEHIHQYAGIDRAVSETLSLVDINVVIIEMNDYLMK-----------------------------------TSDLMMMVMRKINNDESIDHIVYFKFEQLDK------IEPSKLTEFINVLSVLEKSNNIAFKVLIYSN----SSLLSTSLKKKLNTKYTVFEMPILTCAQEQEYLKKMIKFTFDSGSKLLQSYNSLVTCQLNNKESNLAIFFEFLKVFPHPFTYLFNAYTEIIVQSRTFDELLDKIRNRLTIKNYPH 373
                                    77        87        97       107       117       127       137       147   |     -         -         -       187       197       207       217      |227       237       247      |  - |     267       277       287       297       307       317       327       337       347       357       367      
                                                                                                             151                                 187                           217    224                           254  259
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4BJ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BJ1)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (RIF2_YEAST | Q06208)
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).
    GO:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
biological process
    GO:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
    GO:0007004    telomere maintenance via telomerase    The maintenance of proper telomeric length by the addition of telomeric repeats by telomerase.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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.
    GO:0070187    shelterin complex    A nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex is known to contain TERF1, TERF2, POT1, RAP1, TINF2 and ACD in mammalian cells, and Pot1, Tpz1, Rap1, Rif1, Rif2 and Taz1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1, which acts as an effector molecule along with Ccq1.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIF2_YEAST | Q06208: 4bj5 4bj6

(-) Related Entries Specified in the PDB File

4bj5 CRYSTAL STRUCTURE OF RIF2 IN COMPLEX WITH THE C- TERMINAL DOMAIN OF RAP1 (RAP1-RCT)
4bj6 CRYSTAL STRUCTURE RIF2 IN COMPLEX WITH THE C-TERMINAL DOMAIN OF RAP1 (RAP1-RCT)
4bjs CRYSTAL STRUCTURE OF THE RIF1 C-TERMINAL DOMAIN (RIF1 -CTD) FROM SACCHAROMYCES CEREVISIAE
4bjt CRYSTAL STRUCTURE OF THE RAP1 C-TERMINAL DOMAIN (RAP1 -RCT) IN COMPLEX WITH THE RAP1 BINDING MODULE OF RIF1 (RIF1-RBM)