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(-) Description

Title :  TERNARY COMPLEX OF HUMAN DNA POLYMERASE THETA C-TERMINAL DOMAIN BINDING DDGTP OPPOSITE DCMP
 
Authors :  K. E. Zahn, S. Doublie
Date :  22 Nov 14  (Deposition) - 18 Mar 15  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.90
Chains :  Asym. Unit :  A,B,E,F,G,H
Biol. Unit 1:  A,E,F  (1x)
Biol. Unit 2:  B,G,H  (1x)
Keywords :  Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Zahn, A. M. Averill, P. Aller, R. D. Wood, S. Doublie
Human Dna Polymerase Theta Grasps The Primer Terminus To Mediate Dna Repair.
Nat. Struct. Mol. Biol. V. 22 304 2015
PubMed-ID: 25775267  |  Reference-DOI: 10.1038/NSMB.2993

(-) Compounds

Molecule 1 - DNA POLYMERASE THETA
    Chains: A, B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO3
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1815-2590
    Gene: POLQ, POLH
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA POLYMERASE ETA
 
Molecule 2 - DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*G)-3')
    Chains: E, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
    Chains: F, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABEFGH
Biological Unit 1 (1x): A EF  
Biological Unit 2 (1x):  B  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1DG32Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1DG31Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1DG31Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:2427binding site for residue GOL A 2601
2AC2SOFTWAREASP A:1966 , ILE A:1968 , GLN A:1969 , VAL A:2232binding site for residue GOL A 2602
3AC3SOFTWAREASP A:2330 , TYR A:2331 , ASP A:2540 , DG3 A:2604binding site for residue MG A 2603
4AC4SOFTWAREASP A:2330 , ARG A:2379 , LYS A:2383 , GLN A:2384 , TYR A:2387 , ASP A:2540 , MG A:2603 , DC E:4 , DC E:5 , DG F:13binding site for residue DG3 A 2604
5AC5SOFTWAREMET B:2427binding site for residue GOL B 2601
6AC6SOFTWAREASP B:1966 , ILE B:1968 , GLN B:1969 , VAL B:2232 , SER B:2233binding site for residue GOL B 2602
7AC7SOFTWAREASP B:2330 , TYR B:2331 , ASP B:2540 , DG3 B:2604binding site for residue MG B 2603
8AC8SOFTWAREASP B:2330 , GLN B:2333 , GLU B:2335 , ARG B:2379 , LYS B:2383 , GLN B:2384 , TYR B:2387 , TYR B:2391 , ASP B:2540 , MG B:2603 , DC G:4 , DC G:5 , DG H:13binding site for residue DG3 B 2604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X0Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X0Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4X0Q)

(-) 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:625
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhhhhhhhhhh..eeeee............eeeee......eeee........hhhhhhhhhhhh.......eee...hhhhhhhhhhh.......eeehhhhhhhhhh......hhhhhhhhh...hhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhee......eee..................hhhhh...eeee...eeee.hhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....eeeeeee..eeeeeee..hhhhhhhhhhhhhhh.........eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4x0q A 1824 SLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRDDTLVVGLAVCWGGRDAYYFSLLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGMETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPQFSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQNVPRDFEIKMGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLETFHSTFKSHGHREGMLQSDCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELKDFDV 2590
                                  1833      1843      1853      1898      1908      1935      1945      1955      1965      1975      1985      1995      2005      2015      2025      2035      2045      2055      2065      2075      2085      2095      2105      2115      2125      2135      2145|     2185      2195      2205      2215      2225      2235      2245      2255    ||2311      2321      2331      2341      2351      2361      2371      2381      2391      2401      2411      2421      2431      2441      2451      2461      2471      2481      2491      2501      2511||    2535      2545      2555      2565      2575      2585     
                                                             1860|                 1917|                                                                                                                                                                                                              2145|                                                                                2260|                                                                                                                                                                                                         2512|                                                               
                                                              1896                  1935                                                                                                                                                                                                               2176                                                                                 2307                                                                                                                                                                                                          2527                                                               


Chain B from PDB  Type:PROTEIN  Length:625
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....hhhhhhhhhhhhhh..eeeee............eeeee......eeee........hhhhhhhhhhhh.......eee...hhhhhhhhhhh.......eeehhhhhhhhhh......hhhhhhhhh...hhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhee......eee..................hhhhh...eeee...eeee.hhhhh.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.....eeeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4x0q B 1824 SLSIIDVASDQNLFQTFIKEWRCKKRFSISLACEKIRDDTLVVGLAVCWGGRDAYYFSLLDPSLTLKDRMWYLQSCLRKESDKECSVVIYDFIQSYKILLLSCGISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGMETSQGIQSLGLNAGSEHSGRYRASVESILIFNSMNQLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPQFSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPVSQSHTATGRITFTEPNIQNVPRDFEIKMGMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLETFHSTFKSHGHREGMLQSDCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELKDFDV 2590
                                  1833      1843      1853      1898      1908      1935      1945      1955      1965      1975      1985      1995      2005      2015      2025      2035      2045      2055      2065      2075      2085      2095      2105      2115      2125      2135      2145|     2185      2195      2205      2215      2225      2235      2245      2255    ||2311      2321      2331      2341      2351      2361      2371      2381      2391      2401      2411      2421      2431      2441      2451      2461      2471      2481      2491      2501      2511||    2535      2545      2555      2565      2575      2585     
                                                             1860|                 1917|                                                                                                                                                                                                              2145|                                                                                2260|                                                                                                                                                                                                         2512|                                                               
                                                              1896                  1935                                                                                                                                                                                                               2176                                                                                 2307                                                                                                                                                                                                          2527                                                               


Chain E from PDB  Type:DNA  Length:13
                                              
                4x0q E    1 CGTCCAATGACAG   13
                                    10   


Chain F from PDB  Type:DNA  Length:9
                                          
                4x0q F    5 CTGTCATTG   13


Chain G from PDB  Type:DNA  Length:13
                                              
                4x0q G    1 CGTCCAATGACAG   13
                                    10   


Chain H from PDB  Type:DNA  Length:9
                                          
                4x0q H    5 CTGTCATTG   13
   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 4X0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X0Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X0Q)

(-) Gene Ontology  (27, 27)

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 Related Entries

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        DPOLQ_HUMAN | O75417: 4x0p 5a9f 5a9j 5aga

(-) Related Entries Specified in the PDB File

4x0p