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(-) Description

Title :  STRUCTURAL BASIS OF HUMAN CLAMP SLIDING ON DNA
 
Authors :  M. De March, N. Merino, S. Barrera-Vilarmau, R. Crehuet, S. Onesti, F. A. De Biasio
Date :  03 Jun 16  (Deposition) - 11 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Structural Analysis Human Pcna Dna Complex Sliding, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. De March, N. Merino, S. Barrera-Vilarmau, R. Crehuet, S. Onesti, F. J. Blanco, A. De Biasio
Structural Basis Of Human Pcna Sliding On Dna.
Nat Commun V. 8 13935 2017
PubMed-ID: 28071730  |  Reference-DOI: 10.1038/NCOMMS13935
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROLIFERATING CELL NUCLEAR ANTIGEN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET
    Gene: PCNA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE ORIGINAL SEQUENCE STARTS FROM 1_MET. OUR CONSTRUCT HAS N-TER RESIDUES -2_GLY, -1_PRO AND 0_HIS.
    Synonym: PCNA,CYCLIN
 
Molecule 2 - DNA (5'-D(P*AP*TP*AP*CP*GP*AP*TP*GP*GP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*CP*CP*AP*TP*CP*GP*TP*AP*T)-3')
    Chains: E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5L7C)

(-) Sites  (0, 0)

(no "Site" information available for 5L7C)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:135 -B:162

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L7C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L7C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L7C)

(-) Exons   (0, 0)

(no "Exon" information available for 5L7C)

(-) 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:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhh...eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhhh.....eeeeee.....eeeeeee.....eeeeeeee.................eeeeehhhhhhhhhhhhh....eeeeee...eeeeeee...eeeeeeee......eeee...eeeeeehhhhhhhhhhhhhh..eeeee.....eeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l7c A   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPK 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    || 196       206       216       226       236       246        
                                                                                                                                                                                                                  185|                                                              
                                                                                                                                                                                                                   192                                                              


Chain B from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhh...eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhhh.....eeeeee......eeeeee.....eeeeeee..................eeeeeehhhhhhhhhhhhh...eeeeeee..eeeeeeee..eeeeeeee.......eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l7c B   0 HMFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPK 254
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179     ||194       204       214       224       234       244       254
                                                                                                                                                                                                                   185|                                                               
                                                                                                                                                                                                                    191                                                               


Chain C from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhh...eeeeee...eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhhh.....eeeeee.....eeeeeee......eeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeeee..eeeeeeee.....eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5l7c C   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAP 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    || 197       207       217       227       237       247      
                                                                                                                                                                                                                  185|                                                            
                                                                                                                                                                                                                   193                                                            


Chain D from PDB  Type:DNA  Length:10
                                          
                 5l7c D   1 ATACGATGGG  10
                                    10


Chain E from PDB  Type:DNA  Length:10
                                          
                 5l7c E   1 CCCATCGTAT  10
                                    10
   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 5L7C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L7C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L7C)

(-) Gene Ontology  (57, 57)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5l7c)
 

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  5l7c
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  PCNA_HUMAN | P12004
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 Related Entries

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

UniProtKB/Swiss-Prot
        PCNA_HUMAN | P12004: 1axc 1u76 1u7b 1ul1 1vyj 1vym 1w60 2zvk 2zvl 2zvm 3ja9 3p87 3tbl 3vkx 3wgw 4d2g 4rjf 4ztd 5e0t 5e0u 5e0v 5iy4 5mlo 5mlw 5mom

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L7C)