Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE CDT1 C-TERMINAL DOMAIN
 
Authors :  B. I. Khayrutdinov, W. J. Bae, Y. M. Yun, T. Tsuyama, J. J. Kim, E. Hwang, K. -S. Ryu, H. -K. Cheong, C. Cheong, P. A. Karplus, P. Guntert, S. Tada, Y. H. Jeon, Y. Cho
Date :  06 Jul 09  (Deposition) - 13 Oct 09  (Release) - 03 Nov 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Mouse Cdt1, Replication Licensing Factor, Winged Helix Fold, Mcm Binding, Cell Cycle, Dna Replication, Dna-Binding, Nucleus, Phosphoprotein, Proto-Oncogene, Ubl Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. I. Khayrutdinov, W. J. Bae, Y. M. Yun, J. H. Lee, T. Tsuyama, J. J. Kim, E. Hwang, K. -S. Ryu, H. -K. Cheong, C. Cheong, J. -S. Ko, T. Enomoto, P. A. Karplus, P. Guntert, S. Tada, Y. H. Jeon, Y. Cho
Structure Of The Cdt1 C-Terminal Domain: Conservation Of The Winged Helix Fold In Replication Licensing Factors
Protein Sci. V. 18 2252 2009
PubMed-ID: 19722278  |  Reference-DOI: 10.1002/PRO.236
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA REPLICATION FACTOR CDT1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: VECTOR
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 420-557
    Gene: CDT1, RIS2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DOUBLE PARKED HOMOLOG, DUP, RETROVIRAL INSERTION SITE 2 PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KLO)

(-) Sites  (0, 0)

(no "Site" information available for 2KLO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KLO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KLO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KLO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KLO)

(-) Exons   (0, 0)

(no "Exon" information available for 2KLO)

(-) Sequences/Alignments

NMR Structure
   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:138
 aligned with CDT1_MOUSE | Q8R4E9 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:138
                                   429       439       449       459       469       479       489       499       509       519       529       539       549        
           CDT1_MOUSE   420 PAASPSALKGVSQALLERIRAKEVQKQLARMTRCPEQELRLQRLERLPELARVLRNVFVSERKPALTMEVVCARMVDSCQTALSPGEMEKHLVLLAELLPDWLSLHRIRTDTYVKLDKAVDLAGLTARLAHHVHAEGL 557
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeeeee..eeeeee....hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2klo A   1 PAASPSALKGVSQALLERIRAKEVQKQLARMTRCPEQELRLQRLERLPELARVLRNVFVSERKPALTMEVVCARMVDSCQTALSPGEMEKHLVLLAELLPDWLSLHRIRTDTYVKLDKAVDLAGLTARLAHHVHAEGL 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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 2KLO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KLO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KLO)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (CDT1_MOUSE | Q8R4E9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0000076    DNA replication checkpoint    A cell cycle checkpoint that prevents the initiation of nuclear division until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome.
    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:0030174    regulation of DNA-dependent DNA replication initiation    Any process that modulates the frequency, rate or extent of initiation of DNA-dependent DNA replication; the process in which DNA becomes competent to replicate. In eukaryotes, replication competence is established in early G1 and lost during the ensuing S phase.
    GO:0033262    regulation of nuclear cell cycle DNA replication    Any process that modulates the frequency, rate or extent of The DNA-dependent DNA replication that occurs in the nucleus of eukaryotic organisms as part of the cell cycle.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2klo)
 
  Sites
(no "Sites" information available for 2klo)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2klo)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2klo
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CDT1_MOUSE | Q8R4E9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CDT1_MOUSE | Q8R4E9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CDT1_MOUSE | Q8R4E9: 2rqq 2zxx 3a4c

(-) Related Entries Specified in the PDB File

3a4c CRYSTAL STRUCTURE OF CDT1 C-TERMINAL DOMAIN