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(-)Asym./Biol. Unit
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(-) Description

Title :  BINARY COMPLEX OF HUMAN POLYMERASE NU AND DNA WITH THE FINGER DOMAIN CLOSED AND THUMB DOMAIN ROTATED OUT
 
Authors :  Y. -S. Lee, W. Yang
Date :  27 Jan 15  (Deposition) - 11 Mar 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
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(*CP*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
 
Molecule 3 - DNA (5'-D(*GP*AP*TP*CP*TP*GP*AP*CP*GP*CP*TP*AP*G)-3')
    Chains: P
    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 4XVM)

(-) Sites  (0, 0)

(no "Site" information available for 4XVM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Asp A:229 -Gly A:230
2Leu A:234 -Gly A:235
3Asp A:277 -Asp A:278
4Glu A:374 -Lys A:375
5His A:576 -Pro A:577
6Lys A:615 -Gly A:616
7Gln A:832 -Ala A:833

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XVM)

(-) 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:627
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhhhhhhh.eeeeeeee................eeeeeeeee................eeeee.......hhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhh............eehhhhhhhhhh......hhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh...........hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eee.........eee........................hhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhhhhhhhh............eeeeee......ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xvm A 194 KKHFCDIRHLDDWAKSQLIEMLKQAAALVITVMYTDGSTQLGADQTPVSSVRGIVVLVKRQACGPVLEGFVSDDPCIYIQIEHSAIWDQEQEAHQQFARNVLFQTMKCKCPVICFNAKDFVRIVLQFFGNDGSWKHVADFIGLDPRIAAWLIDPSDATPSFEDLVEKYCEKSITVKVNSTYGNSSRNIVNQNVRENLKTLYRLTMDLCSKLKDYGLWQLFRTLELPLIPILAVMESHAIQVNKEEMEKTSALLGARLKELEQEAHFVAGERFLITSNNQLREILFGKLKLHLKYPSTSEAVLNALRDLHPLPKIILEYRQVHKIKSTFVDGLLACMKKGSISSTWNQTGTVTGRLSAKHPNIQGISKHPIQITTPKKILTISPRAMFVSSKGHTFLAADFSQIELRILTHLSGDPELLKLDDVFSTLTSQWKDVPVEQVTHADREQTKKVVYAVVYGAGKERLAACVPIQEAAQFLESFLQKYKKIKDFARAAIAQCHQTGCVVSIMGRRRPLPRIHAHDQQLRAQAERQAVNFVVQGSAADLCKLAMIHVFTAVAASHTLTARLVAQIHDELLFEVEDPQIPECAALVRRTMESLEQVQALELQLQVPLKVSLSAGRSWGHLVPLQ 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 ||    517       527       537       547       557       567       577       587     ||604       614       624       634       644|      660       670       680       690     ||702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       
                                                                                       255|                                                                                                                                                                                                                                  496|                                                                                593|                                        644|                                          696|                                                                                                                                                                
                                                                                        267                                                                                                                                                                                                                                   510                                                                                 601                                         651                                           699                                                                                                                                                                


Chain P from PDB  Type:DNA  Length:13
                                             
                 4xvm P   1 GATTTGACGCTAG  13
                                    10   


Chain T from PDB  Type:DNA  Length:9
                                         
                 4xvm T   1 CTAGCGTCA   9
   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 4XVM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4xvm)
 
  Cis Peptide Bonds
    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 ]  
    Leu A:234 - Gly A:235   [ RasMol ]  
    Lys A:615 - Gly A:616   [ RasMol ]  
 

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  4xvm
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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 4xvl

(-) Related Entries Specified in the PDB File

4xvi 4xvk 4xvl