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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SLD3/TRESLIN DOMAIN FROM YEAST SLD3
 
Authors :  H. Itou, H. Araki, Y. Shirakihara
Date :  05 Sep 13  (Deposition) - 20 Aug 14  (Release) - 17 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Replication Regulator, Cdc45-Binding, Alpha Helical (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Itou, S. Muramatsu, Y. Shirakihara, H. Araki
Crystal Structure Of The Homology Domain Of The Eukaryotic Dna Replication Proteins Sld3/Treslin.
Structure V. 22 1341 2014
PubMed-ID: 25126958  |  Reference-DOI: 10.1016/J.STR.2014.07.001

(-) Compounds

Molecule 1 - DNA REPLICATION REGULATOR SLD3
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 148-430
    Gene: SLD3, YGL113W, G2980
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric Unit (2, 27)
No.NameCountTypeFull Name
1EDO24Ligand/Ion1,2-ETHANEDIOL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 17)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:160 , LYS A:164 , TYR A:178 , SER A:182 , ASN A:183 , ARG A:186 , ASN C:290BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREASN A:255 , SER A:256 , SER A:257 , THR A:258 , ILE A:259 , EDO A:515 , PRO B:175 , GLU B:387 , TYR B:396BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWARESER A:268 , ILE A:271 , LYS A:272 , ALA A:350 , ASP A:354 , LEU A:390 , HOH A:617BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREARG A:221 , HIS A:222 , ARG A:225 , LEU A:226 , LEU A:227 , CYS A:263 , LYS A:267 , EDO A:514BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREARG A:225 , ALA A:260 , CYS A:263 , VAL A:264 , EDO A:514BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWARELYS A:158 , ILE A:161 , GLU A:162 , MET A:207 , LYS A:210 , PHE A:211BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREVAL A:265 , SER A:268 , ARG A:269 , LYS A:272 , ALA A:388 , HOH A:633BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWARELYS A:267 , ARG A:349 , LEU A:353 , EDO A:517 , HOH A:603 , HOH A:656BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREGLU A:162 , TYR A:166 , EDO A:510BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWARETYR A:166 , LEU A:213 , ARG A:221 , EDO A:509 , HOH A:608 , HOH A:632 , HOH A:640BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWARECYS A:351 , ASP A:354 , ILE A:355 , LEU A:417 , EDO A:516 , HOH A:612 , LEU B:228 , ILE B:259BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREASN A:224 , LEU A:226 , GLU A:229 , EDO B:504BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWARETYR A:154 , SER A:155 , PRO A:157 , ARG A:186 , THR A:190BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWAREHIS A:222 , CYS A:263 , VAL A:264 , EDO A:504 , EDO A:505BINDING SITE FOR RESIDUE EDO A 514
15BC6SOFTWAREARG A:225 , SER A:256 , ILE A:259 , ALA A:260 , EDO A:502 , ALA B:177 , TYR B:396 , TYR B:401 , HOH B:604BINDING SITE FOR RESIDUE EDO A 515
16BC7SOFTWARELEU A:417 , LYS A:418 , EDO A:511 , HOH A:612 , ASN B:224 , ARG B:225 , HOH B:608BINDING SITE FOR RESIDUE EDO A 516
17BC8SOFTWARELYS A:267 , ILE A:352 , LEU A:353 , LEU A:356 , EDO A:508BINDING SITE FOR RESIDUE EDO A 517
18BC9SOFTWAREARG A:240 , LYS A:241 , TYR B:160 , TYR B:178 , SER B:182 , ASN B:183 , ARG B:186 , HOH B:644 , HOH B:686BINDING SITE FOR RESIDUE SO4 B 501
19CC1SOFTWAREASP B:167 , ALA B:168 , SER B:171 , THR B:174 , TYR B:178 , EDO B:503 , HOH B:606 , HOH B:607BINDING SITE FOR RESIDUE EDO B 502
20CC2SOFTWARELYS B:164 , ASP B:167 , TYR B:178 , ASN B:183 , EDO B:502BINDING SITE FOR RESIDUE EDO B 503
21CC3SOFTWAREASN A:224 , EDO A:512 , LYS B:181 , TYR B:401 , HOH B:650BINDING SITE FOR RESIDUE EDO B 504
22CC4SOFTWAREVAL B:265 , SER B:268 , ARG B:269 , HIS B:377 , ILE B:381 , EDO B:507BINDING SITE FOR RESIDUE EDO B 505
23CC5SOFTWAREARG B:221 , HIS B:222 , ARG B:225 , LEU B:226 , LEU B:227 , CYS B:263 , HOH B:646BINDING SITE FOR RESIDUE EDO B 506
24CC6SOFTWAREILE B:172 , HIS B:173 , HIS B:377 , ASN B:380 , ALA B:388 , EDO B:505 , EDO B:509BINDING SITE FOR RESIDUE EDO B 507
25CC7SOFTWARELYS B:267 , ARG B:349 , HOH B:627BINDING SITE FOR RESIDUE EDO B 508
26CC8SOFTWARELYS A:254 , ASN A:255 , SER A:256 , HOH A:606 , HIS B:173 , EDO B:507 , HOH B:605BINDING SITE FOR RESIDUE EDO B 509
27CC9SOFTWARETYR C:160 , TYR C:178 , SER C:182 , ASN C:183 , ARG C:186BINDING SITE FOR RESIDUE SO4 C 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WI3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WI3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WI3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WI3)

(-) Exons   (0, 0)

(no "Exon" information available for 3WI3)

(-) 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:215
 aligned with SLD3_YEAST | P53135 from UniProtKB/Swiss-Prot  Length:668

    Alignment length:268
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413        
           SLD3_YEAST   154 YSDPKEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFRDFEKKYKLKLKKRSLNLTKKGLVRRRSKKKTSEKDKGIERITTSLDYCEQLDLYLDRACILDILLSSETPNPDAIEASNGTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLKGPS 421
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..-------------------------------------------.hhhhhhhhhhhhhhhhhhhhh..----------.hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wi3 A 154 YSDPKEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFRDF-------------------------------------------DYCEQLDLYLDRACILDILLSSET----------GTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLKGPS 421
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293|        -         -         -         -    |  343       353       | -       373       383       393       403       413        
                                                                                                                                                                      294                                         338                    361        372                                                 


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with SLD3_YEAST | P53135 from UniProtKB/Swiss-Prot  Length:668

    Alignment length:266
                                   163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413      
           SLD3_YEAST   154 YSDPKEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFRDFEKKYKLKLKKRSLNLTKKGLVRRRSKKKTSEKDKGIERITTSLDYCEQLDLYLDRACILDILLSSETPNPDAIEASNGTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLKG 419
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh---------------------------------------------.hhhhhhhhhhhhhhhhhhhhh.---------...hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wi3 B 154 YSDPKEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFR---------------------------------------------DYCEQLDLYLDRACILDILLSSE---------SNGTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLKG 419
                                   163       173       183       193       203       213       223       233       243       253       263       273       283        |-         -         -         -         -    |  343       353      |  -      |373       383       393       403       413      
                                                                                                                                                                    292                                           338                   360       370                                                 


Chain C from PDB  Type:PROTEIN  Length:205
 aligned with SLD3_YEAST | P53135 from UniProtKB/Swiss-Prot  Length:668

    Alignment length:261
                                   167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417 
           SLD3_YEAST   158 KEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNFRDFEKKYKLKLKKRSLNLTKKGLVRRRSKKKTSEKDKGIERITTSLDYCEQLDLYLDRACILDILLSSETPNPDAIEASNGTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLK 418
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh----------------------------------------------.hhhhhhhhhhhhhhhhhhhhh..----------.hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wi3 C 158 KEYIESKYYDALFSIHTPLAYFVKSNLVRLKNTCRTKYGSDSYKIAYQAMLQKFLLSIVQFKDRHDNRLLLEPFSSPIADEKRKNCLTKFVIQDENKNSSTIADLCVVLKSREIKLQILLLLEIIGLNDLDWNF----------------------------------------------DYCEQLDLYLDRACILDILLSSET----------GTIQEHKKNILDKSKEASLVGFINYVLIPYFNKKVPHAVEFIIQKLK 418
                                   167       177       187       197       207       217       227       237       247       257       267       277       287   |     -         -         -         -         -|      347       357   |     -    |  377       387       397       407       417 
                                                                                                                                                               291                                            338                    361        372
   Legend:   → Mismatch (orange background)
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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 3WI3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WI3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WI3)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SLD3_YEAST | P53135)
molecular function
    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: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:0006268    DNA unwinding involved in DNA replication    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    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.
cellular component
    GO:0031261    DNA replication preinitiation complex    A protein-DNA complex assembled at eukaryotic DNA replication origins immediately prior to the initiation of DNA replication. The preinitiation complex is formed by the assembly of additional proteins onto an existing prereplicative complex. In budding yeast, the additional proteins include Cdc45p, Sld2p, Sld3p, Dpb11p, DNA polymerases, and others; in fission yeast the GINS complex is present.
    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:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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

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