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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIF1 N-TERMINAL DOMAIN (RIF1-NTD) FROM SACCHAROMYCES CEREVISIAE IN COMPLEX WITH DNA
 
Authors :  R. D. Bunker, J. K. Reinert, T. Shi, N. H. Thoma
Date :  05 May 17  (Deposition) - 14 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  6.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Telomere Maintenance, Dna Double-Strand Break Repair, Irregular Helical Repeat, All-Alpha Fold, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mattarocci, J. K. Reinert, R. D. Bunker, G. A. Fontana, T. Shi, D. Klein, S. Cavadini, M. Faty, M. Shyian, L. Hafner, D. Shore, N. H. Thoma, U. Rass
Rif1 Maintains Telomeres And Mediates Dna Repair By Encasin Dna Ends.
Nat. Struct. Mol. Biol. 2017
PubMed-ID: 28604726  |  Reference-DOI: 10.1038/NSMB.3420

(-) Compounds

Molecule 1 - TELOMERE LENGTH REGULATOR PROTEIN RIF1
    Chains: A, B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE (BTI-TN-5B1-4)
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Gene: RIF1, YBR275C, YBR1743
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE S288C
    Organism Taxid: 559292
    Synonym: RAP1-INTERACTING FACTOR 1
 
Molecule 2 - DNA (60-MER)
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DIRECTIONALITY AND SEQUENCE REGISTER OF THE DNA COULD NOT BE ESTABLISHED UNEQUIVOCALLY. DNA DUPLEX MODELED AS POLY-T IN THE MOST PLAUSIBLE ORIENTATION. CHAIN C CONSTRUCT SEQUENCE: ACGCTGCCGAATTCTACCAGTGCCTTGCTAGGACATCTTTGCCCACCTGCAGGTTCACCC.
    Synthetic: YES
 
Molecule 3 - DNA (30-MER)
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DIRECTIONALITY AND SEQUENCE REGISTER OF THE DNA COULD NOT BE ESTABLISHED UNEQUIVOCALLY. DNA DUPLEX MODELED AS POLY-T IN MOST PLAUSIBLE ORIENTATION. CHAIN D CONSTRUCT SEQUENCE: TAGCAAGGCACTGGTAGAATTCGGCAGCGT.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5NW5)

(-) Sites  (0, 0)

(no "Site" information available for 5NW5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5NW5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:1222 -Pro A:1223
2Pro B:1222 -Pro B:1223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NW5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NW5)

(-) Exons   (0, 0)

(no "Exon" information available for 5NW5)

(-) 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:1085
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhh.....hhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhh...hhhhhhh.hhhhh.hhhhhhhhhhhhhhhhh.............hhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhh...hhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5nw5 A  185 ETRVNPRALEYWVSGEIHGLVDNESVSEFKEIIEGGLGILRQESEDYVARRFEVYATFNNIIPILTTKNVNEVDQKFNILIVNIESIIEICIPHLQIAQDTLLSSSEKKNPFVIRLYVQIVRFFSAIMSNFKIVKWLTKRPDLVNKLKVIYRWTTGALRNENSNKIIITAQVSFLRDEKFGTFFLSNEEIKPIISTFTEIMEINSHNLIYEKLLLIRGFLSKYPKLMIETVTSWLPGEVLPRIIIGDEIYSMKILITSIVVLLELLKKCLDFVDEHERIYQCIMLSPVCETIPEKFLSKLPLNSYDSANLDKVTIGHLLTQQIKNYIVVKNDNKIAMDLWLSMTGLLYDSGKRVYDLTSESNKVWFDLNNLCFINNHPKTRLMSIKVWRIITYCICTKISQKNQEGNKSLLSLLRTPFQMTLPYVNDPSAREGIIYHLLGVVYTAFTSNKNLSTDMFELFWDHLITPIYEDYVFKYDSIHLQNVLFTVLHLLIGGKNADVALERKHIHPMSVIASEGVKLKDISSLPPQIIKREYDKIMKVVFQAVEVAISNVNLAHDLILTSLKHLPEDRKDQTHLESFSSLILKVTQNNKDTPIFRDFFGAVTSSFVYTFLDLFLRKNDSSLVNFNIQISKVGISQGNMTLDLLKDVIRKARNETSEFLIIEKFLELDDKKTEVYAQNWVGSTLLPPNISFREFQSLANIVNKVPNENSIENFLDLCLKLSFPVNLFTLLHVSMWSNNNFIYFIQSYVSKNENKLNVDLITLLKTSLPGNPELFSGLLPFLRRNKFMDILEYCIHSNPNLLNSIPDLNSDLLLKLLPRSRASYFAANIKLFKCSEQLTLVRWLLKGQQLEQLNQNFSEIENVLQNASDSELEKSEIIRELLHLAMANPIEPLFSGLLNFCIKNNMADHLDEFCGNMTSEVLFKISPELLLKLLTYKEKPNGKLLAAVIEKIENGDDDYILELLEKIIIQKEIQILEKLKEPLLVFFLNPVSSNMQKHKKSTNMLRELVLLYLTKPLSRSAAKKFFSMLISILPPNPNYQTIDMVNLLIDLIKSHNRKFKDKRTYNATLKTIGKWIQESGVVHQ 1272
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684   ||  697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257      1267     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 688|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  692                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:1085
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................hhhhhhhhhhhhhhh.........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhh...hhhhhhh.hhhhh.hhhhhhhhhhhhhhhhh.............hhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhh.hhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5nw5 B  185 ETRVNPRALEYWVSGEIHGLVDNESVSEFKEIIEGGLGILRQESEDYVARRFEVYATFNNIIPILTTKNVNEVDQKFNILIVNIESIIEICIPHLQIAQDTLLSSSEKKNPFVIRLYVQIVRFFSAIMSNFKIVKWLTKRPDLVNKLKVIYRWTTGALRNENSNKIIITAQVSFLRDEKFGTFFLSNEEIKPIISTFTEIMEINSHNLIYEKLLLIRGFLSKYPKLMIETVTSWLPGEVLPRIIIGDEIYSMKILITSIVVLLELLKKCLDFVDEHERIYQCIMLSPVCETIPEKFLSKLPLNSYDSANLDKVTIGHLLTQQIKNYIVVKNDNKIAMDLWLSMTGLLYDSGKRVYDLTSESNKVWFDLNNLCFINNHPKTRLMSIKVWRIITYCICTKISQKNQEGNKSLLSLLRTPFQMTLPYVNDPSAREGIIYHLLGVVYTAFTSNKNLSTDMFELFWDHLITPIYEDYVFKYDSIHLQNVLFTVLHLLIGGKNADVALEKKHIHPMSVIASEGVKLKDISSLPPQIIKREYDKIMKVVFQAVEVAISNVNLAHDLILTSLKHLPEDRKDQTHLESFSSLILKVTQNNKDTPIFRDFFGAVTSSFVYTFLDLFLRKNDSSLVNFNIQISKVGISQGNMTLDLLKDVIRKARNETSEFLIIEKFLELDDKKTEVYAQNWVGSTLLPPNISFREFQSLANIVNKVPNENSIENFLDLCLKLSFPVNLFTLLHVSMWSNNNFIYFIQSYVSKNENKLNVDLITLLKTSLPGNPELFSGLLPFLRRNKFMDILEYCIHSNPNLLNSIPDLNSDLLLKLLPRSRASYFAANIKLFKCSEQLTLVRWLLKGQQLEQLNQNFSEIENVLQNASDSELEKSEIIRELLHLAMANPIEPLFSGLLNFCIKNNMADHLDEFCGNMTSEVLFKISPELLLKLLTYKEKPNGKLLAAVIEKIENGDDDYILELLEKIIIQKEIQILEKLKEPLLVFFLNPVSSNMQKHKKSTNMLRELVLLYLTKPLSRSAAKKFFSMLISILPPNPNYQTIDMVNLLIDLIKSHNRKFKDKRTYNATLKTIGKWIQESGVVHQ 1272
                                   194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684  ||   697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257      1267     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                687|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 691                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:DNA  Length:30
                                                               
                5nw5 C    1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA   30
                                    10        20        30


Chain D from PDB  Type:DNA  Length:30
                                                               
                5nw5 D    1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT   30
                                    10        20        30
   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 5NW5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NW5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NW5)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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    Pro A:1222 - Pro A:1223   [ RasMol ]  
    Pro B:1222 - Pro B:1223   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIF1_YEAST | P29539: 4bjs 4bjt 5nvr

(-) Related Entries Specified in the PDB File

5nvr 5NVR CONTAINS A SIMILAR RIF1-NTD CONSTRUCT WITHOUT DNA