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(-) Description

Title :  TREX1-DSDNA COMPLEX
 
Authors :  J. M. Fye, S. Harvey, F. W. Perrino, T. Hollis
Date :  10 Mar 15  (Deposition) - 27 May 15  (Release) - 27 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Protein-Dna Complex, Exonuclease, Trex1, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Grieves, J. M. Fye, S. Harvey, J. M. Grayson, T. Hollis, F. W. Perrino
Exonuclease Trex1 Degrades Double-Stranded Dna To Prevent Spontaneous Lupus-Like Inflammatory Disease.
Proc. Natl. Acad. Sci. Usa V. 112 5117 2015
PubMed-ID: 25848017  |  Reference-DOI: 10.1073/PNAS.1423804112

(-) Compounds

Molecule 1 - THREE-PRIME REPAIR EXONUCLEASE 1
    Chains: A, B, C, D
    EC Number: 3.1.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTAGAMI 2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 5-235
    Gene: TREX1
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: 3'-5' EXONUCLEASE TREX1,DNASE III
 
Molecule 2 - DNA (24-MER)
    Chains: E, G
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*GP*TP*GP*CP*TP*GP*AP*CP*GP*TP*CP*AP*GP*CP*AP*CP*GP*AP*CP*G)-3')
    Chains: F, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1DT1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1DT-1Ligand/IonTHYMIDINE-5'-MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:18 , HOH A:401 , DC E:23 , DG E:24binding site for residue MG A 301
2AC2SOFTWAREASN B:18 , HOH B:403 , HOH B:406 , HOH B:407 , DC F:23 , DG F:24binding site for residue MG B 301
3AC3SOFTWAREASN C:18 , HOH C:403 , HOH C:405 , DC H:23 , DG H:24binding site for residue MG C 301
4AC4SOFTWAREASN D:18 , HIS D:124 , HOH D:401 , DC G:23 , DG G:24binding site for residue MG D 301
5AC5SOFTWAREARG B:128 , DG F:21 , DA F:22 , DC F:23 , DG H:21binding site for residue DT H 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1His A:53 -Pro A:54
2Gln A:117 -Pro A:118
3His B:53 -Pro B:54
4Gln B:117 -Pro B:118
5His C:53 -Pro C:54
6Gln C:117 -Pro C:118
7His D:53 -Pro D:54
8Gln D:117 -Pro D:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YNQ)

(-) 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:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhhhh.......hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ynq A   5 TLPHGHMQTLIFLNLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASNGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGT 235
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164 ||    178       188       198       208       218       228       
                                                                                                                                                                                           166|                                                                
                                                                                                                                                                                            171                                                                


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee.........eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhhhh......hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ynq B   5 TLPHGHMQTLIFLNLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSPRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYG 234
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164   ||  179       189       199       209       219       229     
                                                                                                                                                                                             168|                                                            
                                                                                                                                                                                              174                                                            


Chain C from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhhh.........hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ynq C   5 TLPHGHMQTLIFLNLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASSGSRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGT 235
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164  ||   178       188       198       208       218       228       
                                                                                                                                                                                            167|                                                               
                                                                                                                                                                                             172                                                               


Chain D from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee..hhhhh..eeeeeeeeeehhhhhh..................eeeeee.......hhhhhhhh..hhhhhhhh.....hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhh..........eeeehhhhhhhhh.......hhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhee.hhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ynq D   5 TLPHGHMQTLIFLNLEATGLPSSRPEVTELCLLAVHRRALENTSISQGHPPPVPRPPRVVDKLSLCIAPGKACSPGASEITGLSKAELEVQGRQRFDDNLAILLRAFLQRQPQPCCLVAHNGDRYDFPLLQTELARLSTPSPLDGTFCVDSIAALKALEQASRKSYSLGSIYTRLYWQAPTDSHTAEGDVLTLLSICQWKPQALLQWVDEHARPFSTVKPMYGT 235
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164||     181       191       201       211       221       231    
                                                                                                                                                                                          165|                                                              
                                                                                                                                                                                           173                                                              


Chain E from PDB  Type:DNA  Length:21
                                                     
                 4ynq E   4 CGTGCTGACGTCAGCACGACG  24
                                    13        23 


Chain F from PDB  Type:DNA  Length:20
                                                    
                 4ynq F   5 GTGCTGACGTCAGCACGACG  24
                                    14        24


Chain G from PDB  Type:DNA  Length:21
                                                     
                 4ynq G   4 CGTGCTGACGTCAGCACGACG  24
                                    13        23 


Chain H from PDB  Type:DNA  Length:21
                                                     
                 4ynq H   5 GTGCTGACGTCAGCACGACGT 101
                                    14        24|
                                              24|
                                              101
   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 4YNQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

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  4ynq
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  TREX1_MOUSE | Q91XB0
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 Related Entries

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

UniProtKB/Swiss-Prot
        TREX1_MOUSE | Q91XB0: 2ioc 2o4g 2o4i 2oa8 3b6o 3b6p 3mxi 3mxj 3mxm 3u3y 3u6f

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4YNQ)