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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PCNA IN COMPLEX WITH ZRANB3 APIM MOTIF PEPTIDE
 
Authors :  A. Ariza
Date :  07 Dec 16  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  D  (1x)
Biol. Unit 4:  F  (1x)
Keywords :  Endonuclease, Metalloprotein, Pcna, Dna-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sebesta, C. D. O. Cooper, A. Ariza, C. J. Carnie, D. Ahel
Structural Insights Into The Function Of Zranb3 In Replication Stress Response.
Nat Commun V. 8 15847 2017
PubMed-ID: 28621305  |  Reference-DOI: 10.1038/NCOMMS15847

(-) Compounds

Molecule 1 - PROLIFERATING CELL NUCLEAR ANTIGEN
    Chains: A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PCNA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PCNA,CYCLIN
 
Molecule 2 - APIM MOTIF PEPTIDE
    Chains: B, D, F
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):    D  
Biological Unit 4 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:53 , GLU A:238 , LYS A:240 , GLY A:245 , HIS A:246binding site for residue SO4 A 301
2AC2SOFTWAREALA A:82 , GLY A:83 , ASN A:84 , GLU A:85 , ARG C:146binding site for residue SO4 A 302
3AC3SOFTWARELYS A:190 , GLU A:191 , ARG C:53 , LYS C:240 , GLY C:245 , HIS C:246 , HOH C:413binding site for residue SO4 C 301
4AC4SOFTWAREALA C:82 , GLY C:83 , ASN C:84 , ARG E:146binding site for residue SO4 C 302
5AC5SOFTWAREARG E:53 , LYS E:240 , GLY E:245 , HIS E:246binding site for residue SO4 E 301
6AC6SOFTWAREARG A:146 , ASN E:84 , HOH E:412binding site for residue SO4 E 302
7AC7SOFTWARESER E:152 , ASP E:156 , LEU E:209 , ARG E:210 , HOH E:416binding site for residue SO4 E 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MLW)

(-) 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:253
                                                                                                                                                                                                                                                                                              
               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.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeeee..eeeeeeee..........eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5mlw A    1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI  255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     ||192       202       212       222       232       242       252   
                                                                                                                                                                                                                   186|                                                                  
                                                                                                                                                                                                                    189                                                                  


Chain B from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                5mlw B 1069 GSDITRFLVKK 1079
                                  1078 


Chain C from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                         
               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.....eeeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeeee..eeeeeeee.....eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5mlw C    1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKI  255
                                    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:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                5mlw D 1069 GSDITRFLVKK 1079
                                  1078 


Chain E from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhh...eeeeeee..eeeeeee.....eeeeeeee.hhh.eeee...eeeeeehhhhhhhhhh.....eeeeee.....eeeeeee.....eeeeeeee.................eeeeeehhhhhhhhhhhhh...eeeeee...eeeeeeee..eeeeeeee.........eeee...eeeeeehhhhhhhhhhhhhh.eeeeee.....eeeeeee...eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5mlw E    1 MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDEAVTIEMNEPVQLTFALRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPKIE  256
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       193       203       213       223       233       243       253   
                                                                                                                                                                                                                      189|                                                               
                                                                                                                                                                                                                       193                                                               


Chain F from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ...hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                5mlw F 1069 GSDITRFLVK 1078
                                  1078
   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 5MLW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (57, 57)

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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 5l7c 5mlo 5mom

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