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(-) Description

Title :  COMPUTATIONAL DESIGN OF CO-ASSEMBLING PROTEIN-DNA NANOWIRES
 
Authors :  Y. Mou, S. L. Mayo
Date :  08 Jul 14  (Deposition) - 29 Jul 15  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
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 :  Helix-Turn-Helix, Dna-Binding Protein, Double-Stranded Dna, De Novo Design-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Mou, J. Y. Yu, T. M. Wannier, C. L. Guo, S. L. Mayo
Computational Design Of Co-Assembling Protein-Dna Nanowires
Nature V. 525 230 2015
PubMed-ID: 26331548  |  Reference-DOI: 10.1038/NATURE14874

(-) Compounds

Molecule 1 - DUALENH
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Other Details: A COMPUTATIONALLY DESIGNED PROTEIN USING WILD-TYPE ENGRAILED HOMEODOMAIN AS THE BACKBONE TEMPLATE
 
Molecule 2 - DNA (5'- D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3')
    Chains: E, G
    Engineered: YES
    Other Details: A SHORT NA STRAND WITH ENGRAILED HOMEODOMAIN BINDING MOTIFS
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3')
    Chains: F, H
    Engineered: YES
    Other Details: A SHORT NA STRAND WITH ENGRAILED HOMEODOMAIN BINDING MOTIFS
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4QTR)

(-) Sites  (0, 0)

(no "Site" information available for 4QTR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QTR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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Chain A from PDB  Type:PROTEIN  Length:55
                                                                                      
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  4qtr A  5 RTAFSEEQKKALDLAFYFDRYLTPEWRRYLSQRLGLNEAQIKIWFQNKRAKIKKS 59
                                    14        24        34        44        54     


Chain B from PDB  Type:PROTEIN  Length:54
                                                                                     
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  4qtr B  6 TAFSEEQKKALDLAFYFDRYLTPEWRRYLSQRLGLNEAQIKIWFQNKRAKIKKS 59
                                    15        25        35        45        55    


Chain C from PDB  Type:PROTEIN  Length:57
                                                                                        
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                  4qtr C  5 RTAFSEEQKKALDLAFYFDRYLTPEWRRYLSQRLGLNEAQIKIWFQNKRAKIKKSTG 61
                                    14        24        34        44        54       


Chain D from PDB  Type:PROTEIN  Length:55
                                                                                      
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  4qtr D  5 RTAFSEEQKKALDLAFYFDRYLTPEWRRYLSQRLGLNEAQIKIWFQNKRAKIKKS 59
                                    14        24        34        44        54     


Chain E from PDB  Type:DNA  Length:15
                                              
                  4qtr E  1 GTGTAATTTAATTTC 15
                                    10     


Chain F from PDB  Type:DNA  Length:16
                                               
                  4qtr F  1 CGGAAATTAAATTACA 16
                                    10      


Chain G from PDB  Type:DNA  Length:16
                                               
                  4qtr G  1 GTGTAATTTAATTTCC 16
                                    10      


Chain H from PDB  Type:DNA  Length:16
                                               
                  4qtr H  1 CGGAAATTAAATTACA 16
                                    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 4QTR)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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  4qtr
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