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(-) Description

Title :  CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF THE HUMAN DNA PRIMASE LARGE SUBUNIT WITH BOUND DNA TEMPLATE/RNA PRIMER AND MANGANESE ION
 
Authors :  T. H. Tahirov, A. G. Baranovskiy, N. D. Babayeva
Date :  28 Nov 15  (Deposition) - 23 Mar 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Tranferase-Dna-Rna Complex, Dna Primase, Large Subunit, Iron-Sulfur Cluster, Rna, Dna, Primer, Template, Triphosphate, Initiation Site, Manganese, Replication-Dna-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. G. Baranovskiy, N. D. Babayeva, Y. Zhang, J. Gu, Y. Suwa, Y. I. Pavlov T. H. Tahirov
Mechanism Of Concerted Rna-Dna Primer Synthesis By The Huma Primosome.
J. Biol. Chem. V. 291 10006 2016
PubMed-ID: 26975377  |  Reference-DOI: 10.1074/JBC.M116.717405

(-) Compounds

Molecule 1 - DNA PRIMASE LARGE SUBUNIT
    Chains: A, B
    EC Number: 2.7.7.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 266-456
    Gene: PRIM2, PRIM2A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA PRIMASE 58 KDA SUBUNIT,P58
 
Molecule 2 - RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3')
    Chains: C, E
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CONTAINS 5'-TRIPHOSPHATE
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3')
    Chains: D, F
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A CD  
Biological Unit 2 (1x):  B  EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GTP2Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION
3SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GTP1Mod. NucleotideGUANOSINE-5'-TRIPHOSPHATE
2MN-1Ligand/IonMANGANESE (II) ION
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:286 , CYS A:287 , CYS A:367 , CYS A:384 , CYS A:424 , LEU A:441binding site for residue SF4 A 501
2AC2SOFTWAREPRO B:285 , PRO B:286 , CYS B:287 , CYS B:367 , CYS B:384 , PHE B:386 , CYS B:424 , PRO B:444binding site for residue SF4 B 501
3AC3SOFTWAREGTP C:1binding site for residue MN C 101
4AC4SOFTWARETYR B:345 , GTP E:1binding site for residue MN E 101
5AC5SOFTWAREHIS B:300 , ARG B:302 , HIS B:303 , ARG B:306 , TYR B:345 , C E:3 , MN E:101 , DC F:5 , DC F:6 , DA F:7binding site for Di-nucleotide GTP E 1 and G E 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F0S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F0S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F0S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F0S)

(-) Exons   (0, 0)

(no "Exon" information available for 5F0S)

(-) 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:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh............hhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0s A 270 KISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILN 456
                                   279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       


Chain B from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh............hhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f0s B 271 ISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRIL 455
                                   280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     


Chain C from PDB  Type:RNA  Length:6
                                      
                 5f0s C   1 xGCGGC   6
                            |     
                            1-GTP 


Chain D from PDB  Type:DNA  Length:12
                                            
                 5f0s D   1 GCCGCCAACATA  12
                                    10  


Chain E from PDB  Type:RNA  Length:6
                                      
                 5f0s E   1 xGCGGC   6
                            |     
                            1-GTP 


Chain F from PDB  Type:DNA  Length:10
                                          
                 5f0s F   1 GCCGCCAACA  10
                                    10
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  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 5F0S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F0S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F0S)

(-) Gene Ontology  (16, 16)

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  5f0s
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  PRI2_HUMAN | P49643
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRI2_HUMAN | P49643: 3l9q 3q36 4bpu 4bpw 4bpx 4rr2 5dqo 5exr 5f0q 5i7m

(-) Related Entries Specified in the PDB File

5f0q CONTAINS MG INSTEAD OF MN