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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 APHIDICOLIN
 
Authors :  A. G. Baranovskiy, N. D. Babayeva, Y. Suwa, J. Gu, T. H. Tahirov
Date :  17 Apr 14  (Deposition) - 26 Nov 14  (Release) - 07 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym. Unit :  A,B,C,E,F,G
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  E,F,G  (1x)
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, Y. I. Pavlov, T. H. Tahirov
Structural Basis For Inhibition Of Dna Replication By Aphidicolin.
Nucleic Acids Res. V. 42 14013 2014
PubMed-ID: 25429975  |  Reference-DOI: 10.1093/NAR/GKU1209

(-) Compounds

Molecule 1 - DNA POLYMERASE ALPHA CATALYTIC SUBUNIT
    Chains: A, E
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC1
    Expression System Strain: SF-21
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: HUMAN DNA POLYMERASE APHA CATALYTIC CORE DOMAIN RESIDUES 336-1257
    Gene: POLA1, POLA
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA POLYMERASE ALPHA CATALYTIC SUBUNIT P180
 
Molecule 2 - RNA PRIMER
    Chains: B, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA TEMPLATE
    Chains: C, G
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCEFG
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    EFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
12ZE2Ligand/Ion(3R,4R,4AR,6AS,8R,9R,11AS,11BS)-4,9-BIS(HYDROXYMETHYL)-4,11B-DIMETHYLTETRADECAHYDRO-8,11A-METHANOCYCLOHEPTA[A]NAPHTHALENE-3,9-DIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12ZE1Ligand/Ion(3R,4R,4AR,6AS,8R,9R,11AS,11BS)-4,9-BIS(HYDROXYMETHYL)-4,11B-DIMETHYLTETRADECAHYDRO-8,11A-METHANOCYCLOHEPTA[A]NAPHTHALENE-3,9-DIOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12ZE1Ligand/Ion(3R,4R,4AR,6AS,8R,9R,11AS,11BS)-4,9-BIS(HYDROXYMETHYL)-4,11B-DIMETHYLTETRADECAHYDRO-8,11A-METHANOCYCLOHEPTA[A]NAPHTHALENE-3,9-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:864 , TYR A:865 , ASN A:954 , SER A:955 , GLY A:958 , ASP A:1004 , HOH A:1411 , HOH A:1429 , DC B:11 , DG C:111BINDING SITE FOR RESIDUE 2ZE A 1301
2AC2SOFTWARELEU E:864 , TYR E:865 , ASN E:954 , SER E:955 , GLY E:958 , ASP E:1004 , HOH E:1421 , HOH E:1423 , DC F:211 , DG G:311BINDING SITE FOR RESIDUE 2ZE E 1301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Q5V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:576 -Pro A:577
2Lys E:576 -Pro E:577

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Q5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Q5V)

(-) Exons   (0, 0)

(no "Exon" information available for 4Q5V)

(-) 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:865
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee........eeeeeeeee....eeeeeeeee....eeeeeee..eee......eeeee.hhhhhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeee...............eeeee....hhhhhhhhhh.....eeeeee...................hhh.eeee.......eeeeeeeeeeee......eeeeeeeeeeeeee............eeeeee..........hhhhhhhhhh..eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...hhhhhh...........hhhhhhh...eeeehhhhhhhhh.....hhhhhhhhhhh........hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhh.........................eee...eeeeee.hhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...eeee....eeeee....hhhhhhhhhhhhhhhhhh......eeeeeeeeeeeeee..eeeeeeeee.....eeeeeeee.hhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........eeee...hhhhh.hhhhhhhhhhhhhhhhhh........eeeeee.......hhhh.eehhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4q5v 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
                                            
                4q5v B    1 GCCUGGAGCGC   11
                                    10 


Chain C from PDB  Type:DNA  Length:13
                                              
                4q5v C  109 AGGCGCTCCAGGC  121
                                   118   


Chain E from PDB  Type:PROTEIN  Length:865
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.........eeeeeeee.hhhh.eeeeeeee....eeeeeee..eeee....eeeeee.hhhhhhhhhhhhhhhhhh....eeeeee..............eeeeeee...............eeeee....hhhhhhhhhhh....eeeeee...................hhh.eeee.......eeeeeeeeeeee......eeeeeeeeeeeeee............eeeeee..........hhhhhhhhhh..eee..hhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...hhhhhh...........hhhhhhh...eeeehhhhhhhhh.....hhhhhhhhhhh........hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh.........................eee...eeeeee.hhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh...eeee....eeeee....hhhhhhhhhhhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeee.....eeeeeeee.hhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh........eeee.........hhhhhhhhhhhhhhhhhh........eeeeee.......hhhh.eehhhhhhhh.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4q5v E  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 F from PDB  Type:DNA/RNA  Length:11
                                            
                4q5v F  201 GCCUGGAGCGC  211
                                   210 


Chain G from PDB  Type:DNA  Length:13
                                              
                4q5v G  309 AGGCGCTCCAGGC  321
                                   318
   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 4Q5V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Q5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Q5V)

(-) Gene Ontology  (40, 40)

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  4q5v
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  DPOLA_HUMAN | P09884
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 Related Entries

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

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        DPOLA_HUMAN | P09884: 1k0p 1k18 1n5g 4bpx 4qcl 4y97 5exr 5iud

(-) Related Entries Specified in the PDB File

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