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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST CDT1 (N TERMINAL AND MIDDLE DOMAIN), FORM 1.
 
Authors :  V. E. Pye, J. Frigola, J. F. X. Diffley, P. Cherepanov
Date :  14 Nov 16  (Deposition) - 17 May 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Cdt1, Mcm, Winged Helix, Yeast, Dna Replication, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Frigola, J. He, K. Kinkelin, V. E. Pye, L. Renault, M. E. Douglas, D. Remus, P. Cherepanov, A. Costa, J. F. X. Diffley
Cdt1 Stabilizes An Open Mcm Ring For Helicase Loading.
Nat Commun V. 8 15720 2017
PubMed-ID: 28643783  |  Reference-DOI: 10.1038/NCOMMS15720

(-) Compounds

Molecule 1 - CELL DIVISION CYCLE PROTEIN CDT1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-438
    Gene: TAH11, CDT1, SID2, YJR046W, J1641
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: RESIDUES 1-438 OF CDT1 WERE RECOMBINANTLY EXPRESSED AND PURIFIED, RESIDUES WHICH ARE MISSING IN THE STRUCTURE WERE NOT DEFINED IN THE ELECTRON DENSITY.
    Synonym: SIC1 INDISPENSABLE PROTEIN 2,TOPOISOMERASE-A HYPERSENSITIVE PROTEIN 11

 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  (3, 28)

Asymmetric Unit (3, 28)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO43Ligand/IonSULFATE ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:372 , PRO A:386 , LYS A:387 , ARG A:388 , ARG B:101binding site for residue SO4 A 501
02AC2SOFTWARESER A:398 , ARG A:399 , THR A:400 , ARG C:22binding site for residue SO4 A 502
03AC3SOFTWARETHR A:365 , ILE A:366 , ARG A:406 , SER A:409 , TRP A:410 , GLN B:296binding site for residue GOL A 503
04AC4SOFTWARELYS A:151 , TYR A:155 , PHE A:190 , GLN A:285 , GLN A:286 , HOH A:601binding site for residue GOL A 504
05AC5SOFTWAREARG B:22 , GLU B:322 , LYS B:397 , SER B:398 , ARG B:399 , THR B:400binding site for residue SO4 B 501
06AC6SOFTWAREASP A:65 , ARG B:34binding site for residue SO4 B 502
07AC7SOFTWAREVAL B:372 , PRO B:386 , LYS B:387 , ARG B:388binding site for residue SO4 B 503
08AC8SOFTWAREGLN B:91 , LYS B:151 , THR B:153 , VAL B:188 , PHE B:190 , GLN B:285 , GLN B:286 , HOH B:612binding site for residue GOL B 504
09AC9SOFTWAREVAL C:372 , PRO C:386 , LYS C:387 , ARG C:388binding site for residue SO4 C 501
10AD1SOFTWAREARG A:22 , LYS C:397 , SER C:398 , ARG C:399 , THR C:400binding site for residue SO4 C 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ME9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ME9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ME9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ME9)

(-) Exons   (0, 0)

(no "Exon" information available for 5ME9)

(-) 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:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh.................eeee....eeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeee....eee.....eeee..eeeeee......eeeee...eeeeehhhhhhh.........eee.hhhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhh....eeee.....eeee.....hhhhhhh.hhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5me9 A  12 VLRVPVIDLNRVSDEEQLLPVVRAILLQHDTFLLKNYANKAVLDALLAGLTTKDLPDTSQGFDANFTGTLPLEDDVWLEQYIFDTDPQLRFDRKCRNESLCSIYSRLFKLGLFFAQLCVKSVVSSAELQDCISTSHYATKLTRYFNDNDYVTFLPTGVLTIFPCAKAIRYKPSNSWVSIDEPDCLLFHTGTLLARWSQGmHTTSPLQIDPRANIVSLTIWPPLTTPITIANHLLEQQIKAFPKVAQQYYPRELSILRLQDAmKFVKELFTVCETVLSLNALSGVPPELHVLLPQISSmmKRKIVQDDILKLLTIWSDAYVVELNSRGELTmNLPKRDNLTTLTNKSRTLAFVERAESWYQQVIASKDEImTDVPAFKINK 432
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       187       197       207  ||   223       233       243       253       263      |279       289       299       309 |     319       329 ||    342       352       362       372       382|      392       402       412       422       432
                                                                                                                                                                             159|                     210|                       243-MSE                    270|                               311-MSE             331|            350-MSE                          383-MSE                                422-MSE      
                                                                                                                                                                              186                      217                                                   277                                                    335             351-MSE                                                                             


Chain B from PDB  Type:PROTEIN  Length:374
                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..............eeeeehhheeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeee....eee.....eeee..eeeeee.....eeeee...eeeeehhhhhhhh........eee.hhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhh....eeee.....eeee.............hhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5me9 B  12 VLRVPVIDLNRVSDEEQLLPVVRAILLQHDTFLLKNYANKAVLDALLAGLTTKDLPDTSQGFDANFTGTLPLEDDVWLEQYIFDTDPQLRFDRKCRNESLCSIYSRLFKLGLFFAQLCVKSVVSSAELQDCISTSHYATKLTRYFNRDYVTFLPTGVLTIFPCAKAIRYKPNSWVSIDEPDCLLFHTGTLLARWSQGmHTTSPLQIDPRANIVSLTIWPPLTTPISGTIANHLLEQQIKAFPKVAQQYYPRELSILRLQDAmKFVKELFTVCETVLSLNVPPELHVLLPQISSmmKRKIVQDDILKLLTIWSDAYVVELNSRGELTmNLPKRDNLTTLTNKSRTLAFVERAESWYQQVIASKDEImTDVPAFKI 430
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151     ||188       198       208||     225       235       245       255       265     ||279       289       299       309 |     319       336       346   ||  356       366       376      |386       396       406       416     | 426    
                                                                                                                                                                           157|                     209|                       243-MSE                     271|                                311-MSE          328|           350-MSE                          383-MSE                                422-MSE    
                                                                                                                                                                            185                      217                                                    276                                                  336            351-MSE                                                                           


Chain C from PDB  Type:PROTEIN  Length:375
                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh.................eeeee...eeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.......eeeeeeeee...eee.....eeee..eeeeee....eeeee...eeeeehhhhhhhhh.......eee.hhhh.eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhh....eeee.....eeee.....hhhhhhh.hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5me9 C  14 RVPVIDLNRVSDEEQLLPVVRAILLQHDTFLLKNYANKAVLDALLAGLTTKDLPDTSQGFDANFTGTLPLEDDVWLEQYIFDTDPQLRFDRKCRNESLCSIYSRLFKLGLFFAQLCVKSVVSSAELQDCISTSHYATKLTRYFNDDYVTFLPTGVLTIFPCAKAIRYKPSWVSIDEPDCLLFHTGTLLARWSQGmHTTSPLQIDPRANIVSLTIWPPLTTPISGTIANHLLEQQIKAFPKVAQQYYPRELSILRLQDAmKFVKELFTVCETVLSLNALSVPPELHVLLPQISSmmKRKIVQDDILKLLTIWSDAYVVELNSRGELTmNLPKRDNLTTLTNKSRTLAFVERAESWYQQVIASKDEImTDVPAFKIN 431
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153    || 190       200       218       228       238    |  248       258       268  ||   282       292       302       312       322       336       346   ||  356       366       376      |386       396       406       416     | 426     
                                                                                                                                                                          158|                    209|                      243-MSE                     271|                                311-MSE             331|           350-MSE                          383-MSE                                422-MSE     
                                                                                                                                                                           186                     218                                                   276                                                     336            351-MSE
   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 5ME9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ME9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ME9)

(-) Gene Ontology  (11, 11)

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        CDT1_YEAST | P47112: 5h7i 5mea 5meb 5mec 5udb 5v8f 5xf8

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