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(-) Description

Title :  BINARY COMPLEX OF HUMAN POLYMERASE NU AND DNA WITH THE FINGER DOMAIN AJAR
 
Authors :  Y. -S. Lee, W. Yang
Date :  27 Jan 15  (Deposition) - 11 Mar 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Pol Nu, Polymerase, Error-Prone Dna Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. S. Lee, Y. Gao, W. Yang
How A Homolog Of High-Fidelity Replicases Conducts Mutageni Dna Synthesis.
Nat. Struct. Mol. Biol. V. 22 298 2015
PubMed-ID: 25775266  |  Reference-DOI: 10.1038/NSMB.2985

(-) Compounds

Molecule 1 - DNA POLYMERASE NU
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Common: HUMAN
    Expression System Plasmid: PLEXM
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC CORE (UNP RESIDUES 194-859)
    Gene: POLN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DNA (5'-D(*AP*CP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*GP*G)-3')
    Chains: P
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*CP*TP*AP*GP*CP*GP*TP*CP*AP*G)-3')
    Chains: T
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4XVI)

(-) Sites  (0, 0)

(no "Site" information available for 4XVI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XVI)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Asp A:229 -Gly A:230
2Gly A:235 -Ala A:236
3Asp A:277 -Asp A:278
4Glu A:374 -Lys A:375
5His A:576 -Pro A:577
6Lys A:615 -Gly A:616
7Gly A:687 -Ala A:688
8Gln A:832 -Ala A:833
9Ala A:833 -Leu A:834

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XVI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XVI)

(-) Exons   (0, 0)

(no "Exon" information available for 4XVI)

(-) 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:647
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhhh.eeeeeeee................eeeeeeeee..................eeeee.......hhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhh...hhhhh....eehhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh........................hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee...........eeee....eeee.hhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhhhh..ee....ee......eeeeee......ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xvi A 194 KKHFCDIRHLDDWAKSQLIEMLKQAAALVITVMYTDGSTQLGADQTPVSSVRGIVVLVKRQAEGCGPVLEGFVSDDPCIYIQIEHSAIWDQEQEAHQQFARNVLFQTMKCKCPVICFNAKDFVRIVLQFFGNDGSWKHVADFIGLDPRIAAWLIDPSDATPSFEDLVEKYCEKSITVKVNSTYGNSSRNIVNQNVRENLKTLYRLTMDLCSKLKDYGLWQLFRTLELPLIPILAVMESHAIQVNKEEMEKTSALLGARLKELEQEAHFVAGERFLITSNNQLREILFGKLKLHLLSQRNSLPRTGLQKYPSTSEAVLNALRDLHPLPKIILEYRQVHKIKSTFVDGLLACMKKGSISSTWNQTGTVTGRLSAKHPNIQGISKHPIQITTPKKILTISPRAMFVSSKGHTFLAADFSQIELRILTHLSGDPELLKLFQRDDVFSTLTSQWKDVPVEQVTHADREQTKKVVYAVVYGAGKERLAACLGVPIQEAAQFLESFLQKYKKIKDFARAAIAQCHQTGCVVSIMGRRRPLPRIHAHDQQLRAQAERQAVNFVVQGSAADLCKLAMIHVFTAVAASHTLTARLVAQIHDELLFEVEDPQIPECAALVRRTMESLEQVQALELQLQVPLKVSLSAGRSWGHLVPLQ 859
                                   203       213       223       233       243       253   ||  272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592||     609       619       629       639      |652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       
                                                                                         257|                                                                                                                                                                                                                                                                                                                                   593|                                          646|                                                                                                                                                                                                                 
                                                                                          267                                                                                                                                                                                                                                                                                                                                    601                                           650                                                                                                                                                                                                                 


Chain P from PDB  Type:DNA  Length:14
                                              
                 4xvi P   1 ACTCTGACGCTAGG  14
                                    10    


Chain T from PDB  Type:DNA  Length:11
                                           
                 4xvi T   1 CCTAGCGTCAG  11
                                    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 4XVI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XVI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XVI)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4xvi)
 
  Sites
(no "Sites" information available for 4xvi)
 
  Cis Peptide Bonds
    Ala A:833 - Leu A:834   [ RasMol ]  
    Asp A:229 - Gly A:230   [ RasMol ]  
    Asp A:277 - Asp A:278   [ RasMol ]  
    Gln A:832 - Ala A:833   [ RasMol ]  
    Glu A:374 - Lys A:375   [ RasMol ]  
    Gly A:235 - Ala A:236   [ RasMol ]  
    Gly A:687 - Ala A:688   [ RasMol ]  
    His A:576 - Pro A:577   [ RasMol ]  
    Lys A:615 - Gly A:616   [ RasMol ]  
 

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  4xvi
    Family and Domain Information: ProDom | SYSTERS
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    Orientation in Membranes: OPM
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    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
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    Structure Classification: CATH | Dali | SCOP
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Access by UniProt ID/Accession number
  DPOLN_HUMAN | Q7Z5Q5
    Comparative Protein Structure Models: ModBase
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    Protein-protein Interaction: DIP
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  2.7.7.7
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  DPOLN_HUMAN | Q7Z5Q5
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLN_HUMAN | Q7Z5Q5: 4xvk 4xvl 4xvm

(-) Related Entries Specified in the PDB File

4xvk 4xvl 4xvm