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(-) Description

Title :  BINARY COMPLEX OF HUMAN POLYMERASE NU AND DNA WITH THE FINGER DOMAIN OPEN
 
Authors :  Y. -S. Lee, W. Yang
Date :  27 Jan 15  (Deposition) - 11 Mar 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Pol Nu, Polymerase, Error-Prone Dna Synthesis, Transferase-Dna Complex (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(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*CP*G)-3')
    Chains: P
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*CP*GP*TP*AP*GP*CP*GP*TP*CP*A)-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  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2NA1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:310 , CYS A:312 , LYS A:313 , CYS A:314 , ASP A:343 , PHE A:344 , ILE A:345 , ARG A:425binding site for residue MES A 901
2AC2SOFTWAREHIS A:298binding site for residue NA A 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Asp A:229 -Gly A:230
2Asp A:277 -Asp A:278
3Glu A:374 -Lys A:375
4His A:576 -Pro A:577
5Lys A:615 -Gly A:616
6Ser A:648 -Glu A:649
7Ala A:688 -Gly A:689
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 4XVL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XVL)

(-) 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:636
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhhh.eeeeeeee................eeeeeeeee................eeeee.......hhhhhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhh....hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....ee..eee.........eee...........eeee....eeeehhhh.ee.....eeeeeee.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh.............eeeeee......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xvl A 194 KKHFCDIRHLDDWAKSQLIEMLKQAAALVITVMYTDGSTQLGADQTPVSSVRGIVVLVKRQACGPVLEGFVSDDPCIYIQIEHSAIWDQEQEAHQQFARNVLFQTMKCKCPVICFNAKDFVRIVLQFFGNDGSWKHVADFIGLDPRIAAWLIDPSDATPSFEDLVEKYCEKSITVKVNSTYGNSSRNIVNQNVRENLKTLYRLTMDLCSKLKDYGLWQLFRTLELPLIPILAVMESHAIQVNKEEMEKTSALLGARLKELEQEAHFVAGERFLITSNNQLREILFGKLKLHLLSYPSTSEAVLNALRDLHPLPKIILEYRQVHKIKSTFVDGLLACMKKGSISSTWNQTGTVTGRLSAKHPNIQGISKHPIQITTPKKILTISPRAMFVSSKGHTFLAADFSQIELRILTHLSGDPELLKLFQESERDDVFSTLTSQWKDVPVEQVTHADREQTKKVVYAVVYGAGKERLAACLGVPIQEAAQFLESFLQKYKKIKDFARAAIAQCHQTGCVVSIMGRRRPLPRIHAHDQQLRAQAERQAVNFVVQGSAADLCKLAMIHVFTAVAASHTLTARLVAQIHDELLFEVEDPQIPECAALVRRTMESLEQVQALELQLQVPLKVSLSAGRSWGHLVPLQ 859
                                   203       213       223       233       243       253 ||    274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494   ||  516       526       536       546       556       566       576       586      |603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853      
                                                                                       255|                                                                                                                                                                                                                                    498|                                                                               593|                                                                                                                                                                                                                                                                  
                                                                                        267                                                                                                                                                                                                                                     511                                                                                601                                                                                                                                                                                                                                                                  


Chain P from PDB  Type:DNA  Length:14
                                              
                 4xvl P   1 GATCTGACGCTACG  14
                                    10    


Chain T from PDB  Type:DNA  Length:10
                                          
                 4xvl T   2 CGTAGCGTCA  11
                                    11
   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 4XVL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:688 - Gly A:689   [ RasMol ]  
    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 ]  
    His A:576 - Pro A:577   [ RasMol ]  
    Lys A:615 - Gly A:616   [ RasMol ]  
    Ser A:648 - Glu A:649   [ RasMol ]  
 

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  4xvl
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  DPOLN_HUMAN | Q7Z5Q5
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  2.7.7.7
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4xvi 4xvk 4xvm