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(-) Description

Title :  CRYSTAL STRUCTURE OF CDT1/GEMININ COMPLEX
 
Authors :  Y. Cho, C. Lee, B. S. Hong, J. M. Choi
Date :  08 Jan 09  (Deposition) - 17 Feb 09  (Release) - 17 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Coiled-Coil, Cell Cycle, Coiled Coil, Dna Replication Inhibitor, Phosphoprotein, Dna Replication, Dna-Binding, Nucleus, Proto-Oncogene, Ubl Conjugation, Cell Cycle/Replication Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lee, B. S. Hong, J. M. Choi, Y. Kim, S. Watanabe, Y. Ishimi, T. Enomoto, S. Tada, Y. Kim, Y. Cho
Structural Basis For Inhibition Of The Replication Licensing Factor Cdt1 By Geminin
Nature V. 430 913 2004
PubMed-ID: 15286659  |  Reference-DOI: 10.1038/NATURE02813
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GEMININ
    Chains: A, B, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A, PACYC-DUET
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GEMININ COILED-COIL DOMAIN
    Gene: GEMININ, GMNN
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - DNA REPLICATION FACTOR CDT1
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A, PACYC-DUET
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 172-368
    Gene: CDT1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DOUBLE PARKED HOMOLOG, DUP, RETROVIRAL INSERTION SITE 2 PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ZXX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZXX)

(-) 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:70
 aligned with GEMI_MOUSE | O88513 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:70
                                    97       107       117       127       137       147       157
           GEMI_MOUSE    88 KENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYMAEVIERLSN 157
               SCOP domains d2zxxa_ A: Geminin coiled-coil domain                                  SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 2zxx A  88 KENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYmAEVIERLSN 157
                                    97       107       117       127       137       147|      157
                                                                                      148-MSE     


Chain B from PDB  Type:PROTEIN  Length:78
 aligned with GEMI_MOUSE | O88513 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:78
                                    88        98       108       118       128       138       148        
           GEMI_MOUSE    79 TQEAFDLISKENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYMAEVIERLS 156
               SCOP domains d2zxxb_ B: Geminin coiled-coil domain                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 2zxx B  79 TQEAFDLISKENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYmAEVIERLS 156
                                    88        98       108       118       128       138       148        
                                                                                               148-MSE    


Chain C from PDB  Type:PROTEIN  Length:185
 aligned with CDT1_MOUSE | Q8R4E9 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:187
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       
           CDT1_MOUSE   179 KAPAYQRFHALAQPGLPGLVLPYKYQVLVEMFRSMDTIVSMLHNRSETVTFAKVKQGVQEMMRKRFEERNVGQIKTVYPTSYRFRQECNVPTFKDSIKRSDYQLTIEPLLGQEAGGATQLTATCLLQRRQVFRQNLVERVKEQHKVFLASLNPPMAVPDDQLTRWHPRFNVDEVPDIEPAELPQPPV 365
               SCOP domains d2zxxc_ C: DNA replication factor Cdt1                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeeeee.........hhh.eeeeeee.....--.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.......hhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxx C 179 KAPAYQRFHALAQPGLPGLVLPYKYQVLVEmFRSmDTIVSmLHNRSETVTFAKVKQGVQEmmRKRFEERNVGQIKTVYPTSYRFRQECNVPTFKDSIKRSDYQLTIEPLLGQE--GATQLTATCLLQRRQVFRQNLVERVKEQHKVFLASLNPPmAVPDDQLTRWHPRFNVDEVPDIEPAELPQPPV 365
                                   188       198       208|   |  218|      228       238||     248       258       268       278       288  |  | 298       308       318       328    |  338       348       358       
                                                        209-MSE     |                 239-MSE                                             291  |                                    333-MSE                            
                                                            213-MSE |                  240-MSE                                               294                                                                       
                                                                  219-MSE                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:65
 aligned with GEMI_MOUSE | O88513 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:65
                                   102       112       122       132       142       152     
           GEMI_MOUSE    93 SQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYMAEVIERLSN 157
               SCOP domains d2zxxd_ D: Geminin coiled-coil domain                             SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 2zxx D  93 SQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYmAEVIERLSN 157
                                   102       112       122       132       142     | 152     
                                                                                 148-MSE     


Chain E from PDB  Type:PROTEIN  Length:78
 aligned with GEMI_MOUSE | O88513 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:78
                                    88        98       108       118       128       138       148        
           GEMI_MOUSE    79 TQEAFDLISKENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYMAEVIERLS 156
               SCOP domains d2zxxe_ E: Geminin coiled-coil domain                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Geminin-2zxxE01 E:79-156                                                       Pfam domains (1)
           Pfam domains (2) Geminin-2zxxE02 E:79-156                                                       Pfam domains (2)
           Pfam domains (3) Geminin-2zxxE03 E:79-156                                                       Pfam domains (3)
           Pfam domains (4) Geminin-2zxxE04 E:79-156                                                       Pfam domains (4)
         Sec.struct. author ..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 2zxx E  79 TQEAFDLISKENPSSQYWKEVAEQRRKALYEALKENEKLHKEIEQKDSEIARLRKENKDLAEVAEHVQYmAEVIERLS 156
                                    88        98       108       118       128       138       148        
                                                                                               148-MSE    


Chain F from PDB  Type:PROTEIN  Length:184
 aligned with CDT1_MOUSE | Q8R4E9 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:187
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       
           CDT1_MOUSE   179 KAPAYQRFHALAQPGLPGLVLPYKYQVLVEMFRSMDTIVSMLHNRSETVTFAKVKQGVQEMMRKRFEERNVGQIKTVYPTSYRFRQECNVPTFKDSIKRSDYQLTIEPLLGQEAGGATQLTATCLLQRRQVFRQNLVERVKEQHKVFLASLNPPMAVPDDQLTRWHPRFNVDEVPDIEPAELPQPPV 365
               SCOP domains d2zxxf_ F: DNA replication factor Cdt1                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------CDT1-2zxxF01 F:199-362                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) --------------------CDT1-2zxxF02 F:199-362                                                                                                                                              --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhh...eeeeeee.........hhh.eeeeeee.....---....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zxx F 179 KAPAYQRFHALAQPGLPGLVLPYKYQVLVEmFRSmDTIVSmLHNRSETVTFAKVKQGVQEmmRKRFEERNVGQIKTVYPTSYRFRQECNVPTFKDSIKRSDYQLTIEPLLGQE---ATQLTATCLLQRRQVFRQNLVERVKEQHKVFLASLNPPmAVPDDQLTRWHPRFNVDEVPDIEPAELPQPPV 365
                                   188       198       208|   |  218|      228       238||     248       258       268       278       288  |   |298       308       318       328    |  338       348       358       
                                                        209-MSE     |                 239-MSE                                             291 295                                   333-MSE                            
                                                            213-MSE |                  240-MSE                                                                                                                         
                                                                  219-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  (2, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: CDT1] (2)
(-)
Family: CDT1 (2)
(-)
Mus musculus (Mouse) (1)
1aCDT1-2zxxF01F:199-362
1bCDT1-2zxxF02F:199-362
(-)
Clan: no clan defined [family: Geminin] (3)

(-) Gene Ontology  (18, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (GEMI_MOUSE | O88513)
molecular function
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0003714    transcription corepressor activity    A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to repress the transcription of specific genes. Corepressors often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. A third class occludes DNA-binding transcription factor protein-protein interaction domains. A third class of corepressors prevents interactions of DNA bound DNA-binding transcription factor with coactivators.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
biological process
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

Chain C,F   (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.

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 Related Entries

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        CDT1_MOUSE | Q8R4E9: 2klo 2rqq 3a4c

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