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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL REGION OF YEAST CTF4, SELENOMETHIONINE PROTEIN.
 
Authors :  A. C. Simon, L. Pellegrini
Date :  01 Oct 13  (Deposition) - 30 Apr 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Replication, Adaptor Protein, Beta Propeller Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. C. Simon, J. C. Zhou, R. L. Perera, F. Vandeursen, C. Evrin, M. E. Ivanova, M. L. Kilkenny, L. Renault, S. Kjaer, D. Matak-Vinkovic K. Labib, A. Costa, L. Pellegrini
A Ctf4 Trimer Couples The Cmg Helicase To Dna Polymerase Alpha In The Eukaryotic Replisome
Nature V. 510 293 2014
PubMed-ID: 24805245  |  Reference-DOI: 10.1038/NATURE13234

(-) Compounds

Molecule 1 - CTF4
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 31)

Asymmetric/Biological Unit (1, 31)
No.NameCountTypeFull Name
1MSE31Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4C8H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C8H)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:766 -Pro A:767
2Phe B:766 -Pro B:767
3Phe C:766 -Pro C:767

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C8H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C8H)

(-) Exons   (0, 0)

(no "Exon" information available for 4C8H)

(-) 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:431
 aligned with CTF4_YEAST | Q01454 from UniProtKB/Swiss-Prot  Length:927

    Alignment length:452
                                   483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923  
           CTF4_YEAST   474 FRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEGEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQ 925
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee...eeeeeeee..eeeeeeee........eeeee.....eeee...eeeee.....eeeeee.......eeee........eeeeee....eeeee...eeeee.....eeeeee...eeeeeee..eeeeeeee...eeeeeeee.----.eeeeeeee........hhhhhh..hhhhhhhh.....eeee.....eeee....eeeeee........eeeeeeehhhhhhhhh.......eeeeeeeee..eeeeeeee.............eeee......hhhhhhhhhhhhhhh-----------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8h A 474 FRYmPFSPAGTPFGFTDRRYLTmNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSEL----KRYYKRECPLPmSLPNINSDmKKDANLDYYNFNPmGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNmEIWKmSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEmEIRmPVFVKSKLLEENKAILNK-----------------EIQIPVSmAAEEEYLRSKVLSELLTDTLENDGEmYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQ 925
                               |   483       493  |    503       513       523       533       543       553       563       573       583       593       603       613       623       633       643    |  653     | 663    |  673       683       693       703       713       723  |    733       743       753       763       773|   |  783       793  |      -         -|      823       833       843   |   853       863       873       883       893       903       913       923  
                               |                496-MSE                                                                                                                                            643  648        659-MSE  668-MSE       682-MSE                                     726-MSE|                                        774-MSE               796               814      |                       847-MSE                                                                          
                             477-MSE                                                                                                                                                                                                                                                       731-MSE                                        778-MSE                                    821-MSE                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:419
 aligned with CTF4_YEAST | Q01454 from UniProtKB/Swiss-Prot  Length:927

    Alignment length:450
                                   483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923
           CTF4_YEAST   474 FRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEGEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYE 923
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................eeeeee...eeeeeeee..eeeeeeee........eeeee.....eeee...eeeee.....eeeeee.......eeee........eeeeee....eeeee...eeeee.....eeeeee...eeeeeee..eeeeeeee...eeeeeeee.----.eeeeeeee.......-------..hhhhhhhh.....eeee.....eeee....eeeeee........eeeeeeehhhhhhhhh.......eeeeeeeee..eeeeeeee.............eeee......hhhhhhhhh...--------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c8h B 474 FRYmPFSPAGTPFGFTDRRYLTmNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSEL----KRYYKRECPLPmSLPN-------DANLDYYNFNPmGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNmEIWKmSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEmEIRmPVFVKSKLLEENKAI--------------------EIQIPVSmAAEEEYLRSKVLSELLTDTLENDGEmYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYE 923
                               |   483       493  |    503       513       523       533       543       553       563       573       583       593       603       613       623       633       643    |  653     | 663       673       683       693       703       713       723  |    733       743       753       763       773|   |  783       793         -         -|      823       833       843   |   853       863       873       883       893       903       913       923
                             477-MSE            496-MSE                                                                                                                                            643  648        659-MSE     671        682-MSE                                     726-MSE|                                        774-MSE            793                  814      |                       847-MSE                                                                        
                                                                                                                                                                                                                                                                                           731-MSE                                        778-MSE                                    821-MSE                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:425
 aligned with CTF4_YEAST | Q01454 from UniProtKB/Swiss-Prot  Length:927

    Alignment length:452
                                   483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923  
           CTF4_YEAST   474 FRYMPFSPAGTPFGFTDRRYLTMNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPMSLPNINSDMKKDANLDYYNFNPMGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNMEIWKMSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEMEIRMPVFVKSKLLEENKAILNKKNEIGADTEAEEGEEDKEIQIPVSMAAEEEYLRSKVLSELLTDTLENDGEMYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQ 925
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee...eeeeeeee..eeeeeeee........eeeee.....eeee...eeeee.....eeeeee.......eeee........eeeeee....eeeee...eeeee.....eeeeee...eeeeeee..eeeeeeee...eeeeeeeee....eeeeeeeee.......-------..hhhhhhhh.....eeee.....eeee....eeeeee........eeeeeeehhhhhhhhh.......eeeeeeeee..eeeeeeee.............eeee......hhhhhhhhhhhh--------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8h C 474 FRYmPFSPAGTPFGFTDRRYLTmNEVGYVSTVKNSEQYSITVSFFDVGRFREYHFEDLFGYDLCFLNEKGTLFGQSKTGQIQYRPHDSIHSNWTKIIPLQAGERITSVAATPVRVIVGTSLGYFRSFNQFGVPFAVEKTSPIVALTAQNYRVFSVHYSQFHGLSYSLSELGTSSKRYYKRECPLPmSLPN-------DANLDYYNFNPmGIKSLFFSSYGDPCIFGSDNTLLLLSKWRSPEESKWLPILDSNmEIWKmSGGKETTDIHVWPLALAYDTLNCILVKGKHIWPEFPLPLPSEmEIRmPVFVKSKLLEENKAI--------------------EIQIPVSmAAEEEYLRSKVLSELLTDTLENDGEmYGNENEVLAALNGAYDKALLRLFASACSDQNVEKALSLAHELKQDRALTAAVKISERAELPSLVKKINNIREARYEQQ 925
                               |   483       493  |    503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653     | 663       673       683       693       703       713       723  |    733       743       753       763       773|   |  783       793         -         -|      823       833       843   |   853       863       873       883       893       903       913       923  
                             477-MSE            496-MSE                                                                                                                                                            659-MSE     671        682-MSE                                     726-MSE|                                        774-MSE            793                  814      |                       847-MSE                                                                          
                                                                                                                                                                                                                                                                                           731-MSE                                        778-MSE                                    821-MSE
   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 4C8H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C8H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C8H)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CTF4_YEAST | Q01454)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006270    DNA replication initiation    The process in which DNA-dependent DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.
    GO:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0000727    double-strand break repair via break-induced replication    The error-free repair of a double-strand break in DNA in which the centromere-proximal end of a broken chromosome searches for a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template, and progresses to the end of the chromosome.
    GO:0034085    establishment of sister chromatid cohesion    The process in which the sister chromatids of a replicated chromosome become associated with each other during S phase.
    GO:0007064    mitotic sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome are joined along the entire length of the chromosome, from their formation in S phase through metaphase during a mitotic cell cycle. This cohesion cycle is critical for high fidelity chromosome transmission.
    GO:0001302    replicative cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
cellular component
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0043596    nuclear replication fork    The Y-shaped region of a nuclear replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.
    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:0031298    replication fork protection complex    A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CTF4_YEAST | Q01454: 4c8s 4c93 4c95 5hog 5hoi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4C8H)