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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PRIMPOL TERNARY COMPLEX
 
Authors :  O. Rechkoblit, Y. K. Gupta, R. Malik, K. R. Rajashankar, R. E. Johnson, L S. Prakash, A. K. Aggarwal
Date :  02 Aug 16  (Deposition) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,G,H
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,G,H  (1x)
Keywords :  Protein-Dna Complex, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Rechkoblit, Y. K. Gupta, R. Malik, K. R. Rajashankar, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Structure And Mechanism Of Human Primpol, A Dna Polymerase With Primase Activity.
Sci Adv V. 2 01317 2016
PubMed-ID: 27819052  |  Reference-DOI: 10.1126/SCIADV.1601317

(-) Compounds

Molecule 1 - DNA-DIRECTED PRIMASE/POLYMERASE PROTEIN
    Chains: A, B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Taxid: 4932
    Gene: PRIMPOL, CCDC111
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPRIMPOL1,COILED-COIL DOMAIN-CONTAINING PROTEIN 111
 
Molecule 2 - DNA (5'-D(P*TP*CP*GP*CP*(5IU)P*AP*CP*C)-3')
    Chains: C, G
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*GP*TP*AP*GP*CP*(DDG))-3')
    Chains: D, H
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDGH
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
15IU2Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3DDG2Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
15IU1Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3DDG1Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
15IU1Mod. Nucleotide5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3DDG1Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
4DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:76 , TYR A:100 , ASP A:114 , GLU A:116 , LYS A:165 , SER A:167 , HIS A:169 , ARG A:288 , ASN A:289 , ARG A:291 , LYS A:297 , CA A:402 , HOH A:519 , HOH A:530 , DT C:3 , DDG D:14binding site for residue DTP A 401
2AC2SOFTWAREASP A:114 , GLU A:116 , DTP A:401 , HOH A:514binding site for residue CA A 402
3AC3SOFTWAREARG B:76 , TYR B:100 , ASP B:114 , GLU B:116 , LYS B:165 , SER B:167 , HIS B:169 , ARG B:288 , ASN B:289 , ARG B:291 , LYS B:297 , CA B:402 , HOH B:537 , HOH B:544 , DT G:3 , DDG H:14binding site for residue DTP B 401
4AC4SOFTWAREASP B:114 , GLU B:116 , DTP B:401 , HOH B:503binding site for residue CA B 402
5AC5SOFTWAREDG G:5 , DA G:8 , DT H:10 , DA H:11 , DG H:12binding site for Di-nucleotide DC G 6 and 5IU G 7
6AC6SOFTWAREDC G:6 , DC G:9 , DG H:9 , DT H:10 , DA H:11 , DG H:12binding site for Di-nucleotide 5IU G 7 and DA G 8
7AC7SOFTWAREASP B:280 , ARG B:288 , DTP B:401 , DC G:4 , DG G:5 , DG H:12binding site for Di-nucleotide DC H 13 and DDG H 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L2X)

(-) Exons   (0, 0)

(no "Exon" information available for 5L2X)

(-) 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:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhh.....eeeeee.......eeeeeehhhhhhhhhh.......eeee.........eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee.....eeeeeeee....eee.hhhhhhhhhhhhhhhhhhh...hhh.eee.....eee..hhhhh....eee.............ee..............hhhhhhhhhhh..........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l2x A   1 MNRKWEAKLKQIEERASPEEPPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEP 348
                                    10      ||37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197  ||   267       277       287       297       307       317       327       337       347 
                                           17|                                                                                                                                                                  200|                                                                                       
                                            35                                                                                                                                                                   261                                                                                       


Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhhhhhh.......eeeee........eeeeeee.......hhhhhhhhhhhhhhhhhhhhhh...hhh.eeeee.....eeeeeeee....eee.hhhhhhhhhhhhhhhhhh....hhh.eee.....eee..hhhhh...eeee.............ee..............hhhhhhhhhhh..........eee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l2x B  38 PPSIWRLFHRQAQAFNFVKSCKEDVHVFALECKVGDGQRIYLVTTYAEFWFYYKSRKNLLHCYEVIPENAVCKLYFDLEFNKPANPGADGKKMVALLIEYVCKALQELYGVNCSAEDVLNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFLRKILQPALDLLPDLSFLVVKNNMGEKHLFVDLGVYTRNRNFRLYKSSKIGKRVALEVTEDNKFFPIQSKDVSDEYQYFLSSLVSNVRFSDTLRILTCEP 348
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197  ||   267       277       287       297       307       317       327       337       347 
                                                                                                                                                                                            200|                                                                                       
                                                                                                                                                                                             261                                                                                       


Chain C from PDB  Type:DNA  Length:12
                                            
                 5l2x C   2 ATCGCuACCACA  13
                                 |  11  
                                 7-5IU  


Chain D from PDB  Type:DNA  Length:7
                                       
                 5l2x D   8 GGTAGCx  14
                                  |
                                 14-DDG


Chain G from PDB  Type:DNA  Length:8
                                        
                 5l2x G   3 TCGCuACC  10
                                |   
                                |   
                                7-5IU


Chain H from PDB  Type:DNA  Length:7
                                       
                 5l2x H   8 GGTAGCx  14
                                  |
                                 14-DDG
   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 5L2X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L2X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L2X)

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)

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