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(-) Description

Title :  STRUCTURAL AND BIOCHEMICAL STUDIES OF HUMAN PCNA COMPLEXES PROVIDE THE BASIS FOR ASSOCIATION WITH CDK/CYCLIN AND RATIONALE FOR INHIBITOR DESIGN
 
Authors :  G. Kontopidis, S. Wu, D. Zheleva, P. Taylor, C. Mcinnes, D. Lane, P. Fischer, M. D. Walkinshaw
Date :  30 Apr 04  (Deposition) - 13 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,D,E,F  (1x)
Biol. Unit 2:  G,H,I,J,K,L  (1x)
Keywords :  Dna, Replication, Processivity, Oncogene, Dna-Binding Protein, Dna Replication, Dna-Binding Systemic Lupus Erythematosus (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Kontopidis, S. Wu, D. Zheleva, P. Taylor, C. Mcinnes, D. Lane, P. Fischer, M. D. Walkinshaw
Structural And Biochemical Studies Of Human Proliferating Cell Nuclear Antigen Complexes Provide A Rationale For Cyclin Association And Inhibitor Design
Proc. Natl. Acad. Sci. Usa V. 102 1871 2005
PubMed-ID: 15681588  |  Reference-DOI: 10.1073/PNAS.0406540102

(-) Compounds

Molecule 1 - PROLIFERATING CELL NUCLEAR ANTIGEN
    ChainsA, C, E, G, I, K
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPT7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPCNA, CYCLIN
 
Molecule 2 - SMALL PEPTIDE SAVLQKKITDYFHPKK
    ChainsB, D, F, H, J, L
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPT7
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit ABCDEFGHIJKL
Biological Unit 1 (1x)ABCDEF      
Biological Unit 2 (1x)      GHIJKL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1VYJ)

(-) Sites  (0, 0)

(no "Site" information available for 1VYJ)

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1C:135 -C:162
2E:135 -E:162
3G:135 -G:162
4I:135 -I:162
5K:135 -K:162

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VYJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 6)

Asymmetric Unit (1, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071871S228IPCNA_HUMANDisease (ATLD2)369958038A/C/E/G/I/KS228I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071871S228IPCNA_HUMANDisease (ATLD2)369958038A/C/ES228I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071871S228IPCNA_HUMANDisease (ATLD2)369958038G/I/KS228I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 12)

Asymmetric Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCNA_1PS01251 Proliferating cell nuclear antigen signature 1.PCNA_HUMAN34-57
 
 
 
 
 
  6A:34-57
C:34-57
E:34-57
G:34-57
I:34-57
K:34-57
2PCNA_2PS00293 Proliferating cell nuclear antigen signature 2.PCNA_HUMAN61-79
 
 
 
 
 
  6A:61-79
C:61-79
E:61-79
G:61-79
I:61-79
K:61-79
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCNA_1PS01251 Proliferating cell nuclear antigen signature 1.PCNA_HUMAN34-57
 
 
 
 
 
  3A:34-57
C:34-57
E:34-57
-
-
-
2PCNA_2PS00293 Proliferating cell nuclear antigen signature 2.PCNA_HUMAN61-79
 
 
 
 
 
  3A:61-79
C:61-79
E:61-79
-
-
-
Biological Unit 2 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PCNA_1PS01251 Proliferating cell nuclear antigen signature 1.PCNA_HUMAN34-57
 
 
 
 
 
  3-
-
-
G:34-57
I:34-57
K:34-57
2PCNA_2PS00293 Proliferating cell nuclear antigen signature 2.PCNA_HUMAN61-79
 
 
 
 
 
  3-
-
-
G:61-79
I:61-79
K:61-79

(-) Exons   (6, 36)

Asymmetric Unit (6, 36)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003791601ENSE00001480155chr20:5107272-5107146127PCNA_HUMAN-00--
1.2bENST000003791602bENSE00001480145chr20:5100560-5100224337PCNA_HUMAN1-74746A:1-74
C:1-74
E:1-74
G:1-74
I:1-74
K:1-74
74
74
74
74
74
74
1.3ENST000003791603ENSE00001747465chr20:5099512-509941598PCNA_HUMAN74-107346A:74-107
C:74-107
E:74-107
G:74-107
I:74-107
K:74-107
34
34
34
34
34
34
1.4ENST000003791604ENSE00001693283chr20:5099323-509925668PCNA_HUMAN107-129236A:107-129
C:107-129
E:107-129
G:107-129
I:107-129
K:107-129
23
23
23
23
23
23
1.5ENST000003791605ENSE00000906721chr20:5098310-5098116195PCNA_HUMAN130-194656A:130-194
C:130-194
E:130-194
G:130-194
I:130-194
K:130-194
65
65
65
65
65
65
1.6ENST000003791606ENSE00000906720chr20:5096218-5096095124PCNA_HUMAN195-236426A:195-236
C:195-236
E:195-236
G:195-236
I:195-236
K:195-236
42
42
42
42
42
42
1.7ENST000003791607ENSE00000906719chr20:5096008-5095599410PCNA_HUMAN236-261266A:236-257
C:236-257
E:236-257
G:236-260
I:236-257
K:236-257
22
22
22
25
22
22

(-) 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:257
 aligned with PCNA_HUMAN | P12004 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
           PCNA_HUMAN     1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
               SCOP domains d1vyja1 A:1-126 Proliferating cell nuclear antigen (PCNA)                                                                     d1vyja2 A:127-257 Proliferating cell nuclear antigen (PCNA)                                                                         SCOP domains
               CATH domains 1vyjA00 A:1-257  [code=3.70.10.10, no name defined]                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhh....eeeeeee..eeeeeee.....eeeeeeee.hhh........eeeeeehhhhhhhhh......eeeeee.....eeeeeee.....eeeeeeee........ee.......eeeeeehhhhhhhhhhhhhhh.eeeeee...eeeeeeee..eeeeeeee............eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: A:34-57    ---PCNA_2  PDB: A:61-7---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-74 UniProt: 1-74                                      --------------------------------Exon 1.4  PDB: A:107-12Exon 1.5  PDB: A:130-194 UniProt: 130-194                        Exon 1.6  PDB: A:195-236 UniProt: 195-236 --------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.3  PDB: A:74-107           --------------------------------------------------------------------------------------------------------------------------------Exon 1.7 [INCOMPLETE]  Transcript 1 (2)
                 1vyj A   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       

Chain B from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...ee.hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1vyj B   1 SAVLQKKITDYFHPKK  16
                                    10      

Chain C from PDB  Type:PROTEIN  Length:257
 aligned with PCNA_HUMAN | P12004 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
           PCNA_HUMAN     1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
               SCOP domains d1vyjc1 C:1-126 Proliferating cell nuclear antigen (PCNA)                                                                     d1vyjc2 C:127-257 Proliferating cell nuclear antigen (PCNA)                                                                         SCOP domains
               CATH domains 1vyjC00 C:1-257  [code=3.70.10.10, no name defined]                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhh....eeeeee...eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee.....eeeeeeee........ee.......eeeeeehhhhhhhhhhhh....eeeeee...eeeeeee...eeeeeeee............eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: C:34-57    ---PCNA_2  PDB: C:61-7---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: C:1-74 UniProt: 1-74                                      --------------------------------Exon 1.4  PDB: C:107-12Exon 1.5  PDB: C:130-194 UniProt: 130-194                        Exon 1.6  PDB: C:195-236 UniProt: 195-236 --------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.3  PDB: C:74-107           --------------------------------------------------------------------------------------------------------------------------------Exon 1.7 [INCOMPLETE]  Transcript 1 (2)
                 1vyj C   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       

Chain D from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...ee.hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1vyj D   1 SAVLQKKITDYFHPKK  16
                                    10      

Chain E from PDB  Type:PROTEIN  Length:257
 aligned with PCNA_HUMAN | P12004 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
           PCNA_HUMAN     1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
               SCOP domains d1vyje1 E:1-126 Proliferating cell nuclear antigen (PCNA)                                                                     d1vyje2 E:127-257 Proliferating cell nuclear antigen (PCNA)                                                                         SCOP domains
               CATH domains 1vyjE00 E:1-257  [code=3.70.10.10, no name defined]                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhh...eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee.....eeeeeee......eeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeee...eeeeeeee............eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: E:34-57    ---PCNA_2  PDB: E:61-7---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: E:1-74 UniProt: 1-74                                      --------------------------------Exon 1.4  PDB: E:107-12Exon 1.5  PDB: E:130-194 UniProt: 130-194                        Exon 1.6  PDB: E:195-236 UniProt: 195-236 --------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.3  PDB: E:74-107           --------------------------------------------------------------------------------------------------------------------------------Exon 1.7 [INCOMPLETE]  Transcript 1 (2)
                 1vyj E   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       

Chain F from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...ee.hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1vyj F   1 SAVLQKKITDYFHPKK  16
                                    10      

Chain G from PDB  Type:PROTEIN  Length:260
 aligned with PCNA_HUMAN | P12004 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
           PCNA_HUMAN     1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEG 260
               SCOP domains d1vyjg1 G:1-126 Proliferating cell nuclear antigen (PCNA)                                                                     d1vyjg2 G:127-260 Proliferating cell nuclear antigen (PCNA)                                                                            SCOP domains
               CATH domains 1vyjG00 G:1-260  [code=3.70.10.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhh......eeeeeee..eeeeeee.....eeeeeeee.hhh........eeeeeehhhhhhhhh......eeeeee.....eeeeeee.....eeeeeeee........ee.......eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeee...eeeeeeee............eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee..ee..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I-------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: G:34-57    ---PCNA_2  PDB: G:61-7------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: G:1-74 UniProt: 1-74                                      --------------------------------Exon 1.4  PDB: G:107-12Exon 1.5  PDB: G:130-194 UniProt: 130-194                        Exon 1.6  PDB: G:195-236 UniProt: 195-236 ------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.3  PDB: G:74-107           --------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: G:236-260  Transcript 1 (2)
                 1vyj G   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIEDEEG 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain H from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...ee.hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1vyj H   1 SAVLQKKITDYFHPKK  16
                                    10      

Chain I from PDB  Type:PROTEIN  Length:257
 aligned with PCNA_HUMAN | P12004 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
           PCNA_HUMAN     1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
               SCOP domains d1vyji1 I:1-126 Proliferating cell nuclear antigen (PCNA)                                                                     d1vyji2 I:127-257 Proliferating cell nuclear antigen (PCNA)                                                                         SCOP domains
               CATH domains 1vyjI00 I:1-257  [code=3.70.10.10, no name defined]                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhh......eeeeee...eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhhh.....eeeeee.....eeeeeee......eeeeeee........ee.......eeeeeehhhhhhhhhhhhh...eeeeeee..eeeeeeee..eeeeeeee............eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeee....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: I:34-57    ---PCNA_2  PDB: I:61-7---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: I:1-74 UniProt: 1-74                                      --------------------------------Exon 1.4  PDB: I:107-12Exon 1.5  PDB: I:130-194 UniProt: 130-194                        Exon 1.6  PDB: I:195-236 UniProt: 195-236 --------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.3  PDB: I:74-107           --------------------------------------------------------------------------------------------------------------------------------Exon 1.7 [INCOMPLETE]  Transcript 1 (2)
                 1vyj I   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       

Chain J from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ......hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1vyj J   1 SAVLQKKITDYFHPKK  16
                                    10      

Chain K from PDB  Type:PROTEIN  Length:257
 aligned with PCNA_HUMAN | P12004 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
           PCNA_HUMAN     1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
               SCOP domains d1vyjk1 K:1-126 Proliferating cell nuclear antigen (PCNA)                                                                     d1vyjk2 K:127-257 Proliferating cell nuclear antigen (PCNA)                                                                         SCOP domains
               CATH domains 1vyjK00 K:1-257  [code=3.70.10.10, no name defined]                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhh....eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhh......eeeeee....eeeeeeee.....eeeeeeeee.......ee........eeeeehhhhhhhhhhhhh...eeeeee...eeeeeeee..eeeeeeee...................eeeeeehhhhhhhhhhhhhh.eeeeeee..eeeeeeeee...eeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------PCNA_1  PDB: K:34-57    ---PCNA_2  PDB: K:61-7---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: K:1-74 UniProt: 1-74                                      --------------------------------Exon 1.4  PDB: K:107-12Exon 1.5  PDB: K:130-194 UniProt: 130-194                        Exon 1.6  PDB: K:195-236 UniProt: 195-236 --------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.3  PDB: K:74-107           --------------------------------------------------------------------------------------------------------------------------------Exon 1.7 [INCOMPLETE]  Transcript 1 (2)
                 1vyj K   1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIED 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       

Chain L from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ...ee.hhhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 1vyj L   1 SAVLQKKITDYFHPKK  16
                                    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  (1, 12)

Asymmetric Unit
1ad1vyja1A:1-126
1bd1vyja2A:127-257
1cd1vyjc1C:1-126
1dd1vyjc2C:127-257
1ed1vyje1E:1-126
1fd1vyje2E:127-257
1gd1vyjg1G:1-126
1hd1vyjg2G:127-260
1id1vyji1I:1-126
1jd1vyji2I:127-257
1kd1vyjk1K:1-126
1ld1vyjk2K:127-257

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VYJ)

(-) Gene Ontology  (57, 57)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G,I,K   (PCNA_HUMAN | P12004)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070182    DNA polymerase binding    Interacting selectively and non-covalently with a DNA polymerase.
    GO:0030337    DNA polymerase processivity factor activity    An enzyme regulator activity that increases the processivity of polymerization by DNA polymerase, by allowing the polymerase to move rapidly along DNA while remaining topologically bound to it.
    GO:0032405    MutLalpha complex binding    Interacting selectively and non-covalently with the mismatch repair complex MutLalpha.
    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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0032139    dinucleotide insertion or deletion binding    Interacting selectively and non-covalently with double-stranded DNA containing a dinucleotide insertion or deletion.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0030331    estrogen receptor binding    Interacting selectively and non-covalently with an estrogen receptor.
    GO:0035035    histone acetyltransferase binding    Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0000701    purine-specific mismatch base pair DNA N-glycosylase activity    Catalysis of the removal of purines present in mismatches, especially opposite oxidized purines, by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic (AP) site.
    GO:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
biological process
    GO:0042769    DNA damage response, detection of DNA damage    The series of events required to receive a stimulus indicating DNA damage has occurred and convert it to a molecular signal.
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    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:0006271    DNA strand elongation involved in DNA replication    The process in which a DNA strand is synthesized from template DNA during replication by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0034644    cellular response to UV    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0070987    error-free translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions but does not causes an increase in the endogenous mutation level. For S. cerevisiae, RAD30 encodes DNA polymerase eta, which incorporates two adenines. When incorporated across a thymine-thymine dimer, it does not increase the endogenous mutation level.
    GO:0042276    error-prone translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0006272    leading strand elongation    The synthesis of DNA from a template strand in the 5' to 3' direction; leading strand elongation is continuous as it proceeds in the same direction as the replication fork.
    GO:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
    GO:1902990    mitotic telomere maintenance via semi-conservative replication    Any telomere maintenance via semi-conservative replication that is involved in mitotic cell cycle.
    GO:0006297    nucleotide-excision repair, DNA gap filling    Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0032077    positive regulation of deoxyribonuclease activity    Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:0000083    regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
    GO:0031297    replication fork processing    The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
    GO:0046686    response to cadmium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
    GO:0033993    response to lipid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0000722    telomere maintenance via recombination    Any recombinational process that contributes to the maintenance of proper telomeric length.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
    GO:0005663    DNA replication factor C complex    A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.
    GO:0043626    PCNA complex    A protein complex composed of three identical PCNA monomers, each comprising two similar domains, which are joined in a head-to-tail arrangement to form a homotrimer. Forms a ring-like structure in solution, with a central hole sufficiently large to accommodate the double helix of DNA. Originally characterized as a DNA sliding clamp for replicative DNA polymerases and as an essential component of the replisome, and has also been shown to be involved in other processes including Okazaki fragment processing, DNA repair, translesion DNA synthesis, DNA methylation, chromatin remodeling and cell cycle regulation.
    GO:0070557    PCNA-p21 complex    A protein complex that contains the cyclin-dependent protein kinase inhibitor p21WAF1/CIP1 bound to PCNA; formation of the complex inhibits DNA replication.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0043596    nuclear replication fork    The Y-shaped region of a nuclear replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0030894    replisome    A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCNA_HUMAN | P120041axc 1u76 1u7b 1ul1 1vym 1w60 2zvk 2zvl 2zvm 3ja9 3p87 3tbl 3vkx 3wgw 4d2g 4rjf 4ztd 5e0t 5e0u 5e0v 5iy4 5l7c 5mlo 5mlw 5mom

(-) Related Entries Specified in the PDB File

1axc HUMAN PCNA
1u76 CRYSTAL STRUCTURE OF HPCNA BOUND TO RESIDUES 452-466 OF THEDNA POLYMERASE-DELTA-P66 SUBUNIT
1u7b CRYSTAL STRUCTURE OF HPCNA BOUND TO RESIDUES 331-350 OF THEFLAP ENDONUCLEASE-1 (FEN1)
1vym NATIVE HUMAN PCNA
1w60 NATIVE HUMAN PCNA