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(-) Description

Title :  TERNARY COMPLEX OF HUMAN DNA POLYMERASE ETA INSERTING RCTP OPPOSITE AN 8-OXODEOXYGUANOSINE LESION
 
Authors :  Y. Su, M. Egli, F. P. Guengerich
Date :  20 Nov 15  (Deposition) - 13 Jan 16  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Polymerase-Dna Complex, Ribonucleotide Incorporation, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Su, M. Egli, F. P. Guengerich
Mechanism Of Ribonucleotide Incorporation By Human Dna Polymerase Eta.
J. Biol. Chem. V. 291 3747 2016
PubMed-ID: 26740629  |  Reference-DOI: 10.1074/JBC.M115.706226

(-) Compounds

Molecule 1 - DNA POLYMERASE ETA
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid866768
    FragmentUNP RESIDUES 1-432
    GenePOLH, RAD30, RAD30A, XPV
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRAD30 HOMOLOG A,XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN
 
Molecule 2 - DNA (5'-D(*CP*AP*TP*(8OG)P*AP*TP*GP*AP*CP*GP*CP*T)-3')
    ChainsT
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*T)-3')
    ChainsP
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2CA1Ligand/IonCALCIUM ION
3CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
4GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:24 , PRO A:244 , PHE A:247 , SER A:248 , GLY A:276 , GLU A:277 , HOH A:666 , HOH A:682 , HOH A:695 , HOH A:733binding site for residue GOL A 501
2AC2SOFTWAREASP A:13 , MET A:14 , ASP A:115 , CTP T:101binding site for residue CA A 502
3AC3SOFTWAREASP A:13 , MET A:14 , ASP A:15 , CYS A:16 , PHE A:17 , PHE A:18 , ILE A:48 , TYR A:52 , ARG A:55 , ARG A:61 , ASP A:115 , LYS A:231 , CA A:502 , HOH A:694 , HOH A:710 , DT P:8 , DT T:3 , 8OG T:4 , DA T:5 , HOH T:208 , HOH T:210 , HOH T:211 , HOH T:213 , HOH T:219 , HOH T:224 , HOH T:231 , HOH T:233binding site for residue CTP T 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:150 -Pro A:151
2Lys A:231 -Pro A:232
3Ser A:416 -Pro A:417

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EWF)

(-) 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    
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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:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee.hhhhhhhhhhhhhhh...eeeee.......eeeeehhhhhh.......hhhhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhhh....eee....eeeeehhhhhhhhhhhh.....hhhhh..eee.......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeeee.hhhhheeehhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........eeeeee....hhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ewf A  -2 GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSTEWSPPLTMLFLCATKFSAS 432
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147     ||164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404    || 417       427     
                                                                                                                                                                                     153|                                                                                                                                                                                                                                                     409|                   
                                                                                                                                                                                      161                                                                                                                                                                                                                                                      413                   

Chain P from PDB  Type:DNA  Length:8
                                        
                 5ewf P   1 AGCGTCAT   8

Chain T from PDB  Type:DNA  Length:12
                                            
                 5ewf T   1 CATxATGACGCT  12
                               |    10  
                               4-8OG    

   Legend:   → Mismatch (orange background)
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  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 5EWF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLH_HUMAN | Q9Y2532i5o 2lsk 3jaa 3mr2 3mr3 3mr5 3mr6 3si8 3tq1 3wup 4dl2 4dl3 4dl4 4dl5 4dl6 4dl7 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8 4eey 4j9k 4j9l 4j9m 4j9n 4j9o 4j9p 4j9q 4j9r 4j9s 4o3n 4o3o 4o3p 4o3q 4o3r 4o3s 4q8e 4q8f 4rnm 4rnn 4rno 4ru9 4yp3 4yqw 4yr0 4yr2 4yr3 5dg7 5dg8 5dg9 5dga 5dgb 5dlf 5dlg 5dqg 5dqh 5dqi 5ewe 5ewg 5f9l 5f9n 5jum 5kfa 5kfb 5kfc 5kfd 5kfe 5kff 5kfg 5kfh 5kfi 5kfj 5kfk 5kfl 5kfm 5kfn 5kfo 5kfp 5kfq 5kfr 5kfs 5kft 5kfu 5kfv 5kfw 5kfx 5kfy 5kfz 5kg0 5kg1 5kg2 5kg3 5kg4 5kg5 5kg6 5kg7 5l1i 5l1j 5l1k 5l1l 5l9x

(-) Related Entries Specified in the PDB File

5ewe 5ewg