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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF HUMAN DNA POLYMERASE ALPHA IN TERNARY COMPLEX WITH AN RNA-PRIMED DNA TEMPLATE AND DCTP
 
Authors :  A. G. Baranovskiy, Y. Suwa, N. D. Babayeva, J. Gu, T. H. Tahirov
Date :  12 May 14  (Deposition) - 26 Nov 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  B-Family Dna Polymerase, Dna Replication, Transferase-Dna-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. G. Baranovskiy, N. D. Babayeva, Y. Suwa, J. Gu, T. H. Tahirov
Crystal Structure Of Human Dna Polymerase Alpha Catalytic Core In Complex With Dna/Rna And Dcp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA POLYMERASE ALPHA CATALYTIC SUBUNIT
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System PlasmidPFASTBAC1
    Expression System StrainSF-21
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentHUMAN DNA POLYMERASE APHA CATALYTIC CORE DOMAIN RESIDUES 336-1257
    GenePOLA, POLA1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDNA POLYMERASE ALPHA CATALYTIC SUBUNIT P180
 
Molecule 2 - RNA PRIMER
    ChainsB
    EngineeredYES
    Other DetailsENGINEERED SYNTHETIC
    SyntheticYES
 
Molecule 3 - DNA TEMPLATE
    ChainsC
    EngineeredYES
    Other DetailsENGINEERED SYNTHETIC
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4K1Ligand/IonPOTASSIUM ION
5MG1Ligand/IonMAGNESIUM ION
6ZN3Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:860 , PHE A:861 , ASN A:862 , SER A:863 , LEU A:864 , TYR A:865 , ARG A:922 , LYS A:950 , ASP A:1004 , MG A:1302 , ZN A:1303 , HOH A:1430 , HOH A:1446 , HOH A:1448 , HOH A:1470 , HOH A:1475 , HOH A:1597 , HOH A:1601 , DC B:11 , DG C:110 , DG C:111BINDING SITE FOR RESIDUE DCP A 1301
2AC2SOFTWAREASP A:860 , PHE A:861 , ASP A:1004 , DCP A:1301 , ZN A:1303BINDING SITE FOR RESIDUE MG A 1302
3AC3SOFTWAREASP A:860 , ASP A:1004 , DCP A:1301 , MG A:1302 , HOH A:1516 , HOH A:1601BINDING SITE FOR RESIDUE ZN A 1303
4AC4SOFTWAREHIS A:342 , GLU A:500BINDING SITE FOR RESIDUE ZN A 1304
5AC5SOFTWARECYS A:1224 , GLU A:1225 , ILE A:1227 , ILE A:1230 , HOH A:1510BINDING SITE FOR RESIDUE K A 1305
6AC6SOFTWAREVAL A:340 , PHE A:341 , PRO A:504 , ALA A:516 , GLU A:517 , HOH A:1602 , HOH A:1623 , HOH A:1627 , HOH A:1653BINDING SITE FOR RESIDUE 1PE A 1306
7AC7SOFTWARELYS A:437 , TYR A:797 , TYR A:801 , ILE A:802 , VAL A:803 , HOH A:1512BINDING SITE FOR RESIDUE EDO A 1307
8AC8SOFTWAREG B:6 , HOH B:610 , HOH B:615BINDING SITE FOR RESIDUE ZN B 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:576 -Pro A:577

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QCL)

(-) 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:865
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee........eeeeeeeeehhhheeeeeeeee....eeeeeee..eee......eeeee.hhhhhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee...............eeeee....hhhhhhhhhhh....eeeeee.............eeeee.hhh.eeee.......eeeeeeeeeeee......eeeeeeeeeeeeee............eeeeee..........hhhhhhhhhh..eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...hhhhhh...........hhhhhhh...eeeehhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhh.........................eee...eeeeee.hhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....eeeee....hhhhhhhhhhhhhhhhhh......eeeeeeeeeeeeee..eeeeeeeee.....eeeeeeee.hhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhheeee...hhhhh.hhhhhhhhhhhhhhhhhh........eeeeeeee.....hhhh.eehhhhhhhh...eehhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4qcl A  338 EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTLYFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEKNYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELFLMNRKIKGPCWLEVKSPQLLNQPVSWCKAEAMALKPDLVNVIKDVSPPPLVVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVSKPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGHNIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGFGERNATCGRMICDVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYLLEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFLLLHAFYENNYIVPDKQIRKKAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSIIQEFNICFTTVQRVEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQDLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGREILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKLYKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRRDWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQFEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQDGSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDAVLIATWLGLDPT 1244
                                   347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667     ||681       691       701       711       721       731       741       751       761       771       781       791       801      |836       846       856       866       876     ||899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239     
                                                                                                                                                                                                                                                                                                                                                                         673|                                                                                                                               808|                                             882|                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                          678                                                                                                                                834                                              896                                                                                                                                                                                                                                                                                                                                                            

Chain B from PDB  Type:DNA/RNA  Length:11
                                            
                4qcl B    1 GCCUGGAGCGC   11
                                    10 

Chain C from PDB  Type:DNA  Length:13
                                              
                4qcl C  109 AGGCGCTCCAGGC  121
                                   118   

   Legend:   → Mismatch (orange background)
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    → 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 4QCL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:576 - Pro A:577   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLA_HUMAN | P098841k0p 1k18 1n5g 4bpx 4q5v 4y97 5exr 5iud

(-) Related Entries Specified in the PDB File

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