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(-) Description

Title :  STRUCTURE OF HUMAN DICER PLATFORM-PAZ-CONNECTOR HELIX CASSETTE IN COMPLEX WITH 17-MER SIRNA HAVING 5'-P AND UU-3' ENDS (3.1 ANGSTROM RESOLUTION)
 
Authors :  D. K. Simanshu, Y. Tian, D. J. Patel
Date :  01 Nov 13  (Deposition) - 05 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,G,H  (1x)
Biol. Unit 2:  B,E,F  (1x)
Biol. Unit 3:  A,D,G,H  (1x)
Biol. Unit 4:  B,C,E,F  (1x)
Keywords :  Paz Domain, Platform Domain, Connector Helix, Sirna, Rnase Iii Domain, Endoribonuclease, Pre-Mirna, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Tian, D. K. Simanshu, J. B. Ma, J. E. Park, I. Heo, V. N. Kim, D. J. Patel
A Phosphate-Binding Pocket Within The Platform-Paz-Connecto Helix Cassette Of Human Dicer.
Mol. Cell V. 53 606 2014
PubMed-ID: 24486018  |  Reference-DOI: 10.1016/J.MOLCEL.2014.01.003

(-) Compounds

Molecule 1 - ENDORIBONUCLEASE DICER
    Chains: A, B, C, D
    EC Number: 3.1.26.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PLATFORM-PAZ-CONNECTOR HELIX CASSETTE (UNP RESIDUES 765- 1065)
    Gene: DICER, DICER1, HERNA, KIAA0928
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HELICASE WITH RNASE MOTIF, HELICASE MOI
 
Molecule 2 - 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)- 3'
    Chains: E, F, G, H
    Engineered: YES
    Other Details: SIRNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A     GH
Biological Unit 2 (1x):  B  EF  
Biological Unit 3 (1x): A  D  GH
Biological Unit 4 (1x):  BC EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 4NGF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:905 -Lys A:906

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NGF)

(-) 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:260
                                                                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.............hhhhh..eeeeee.........eeee...eeeeeeeeeeee.....hhhhhhhhhhhhhhhh.....eeeeeee...eee...hhhhhh...................eeee..........eeeeeee...............hhhhhhhhhhh.........eeeee..............hhhhhhhhhhhhhhhhheehhh.eee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ngf A  756 QPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRYCVLPLNVVSTLDIDFKFMEDIEKSETKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC 1053
                                   765       775       785       795       805       815       825       835       845   ||  871  ||   884       894|      914       924       934       944       954       964       974       984      1003      1013      1023      1033      1043      1053
                                                                                                                       849|     874|             894|                                                                                     993|                                                  
                                                                                                                        866      878              905                                                                                     1003                                                  


Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.............hhhhh..eeeeee.........eeee...eeeeeeeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeee....eehhhhhhhhh....................eeee..........eeeeeee...............hhhhhhhhhhh.........eeeee.............hhhhhhhhhhhhhhh.eehhh.eee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ngf B  756 QPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRLYCVLPLNVSTLDIDFKFMEDIEKSEYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC 1053
                                   765       775       785       795       805       815       825       835       845    || 870  ||   884       894|      913       923       933       943       953       963       973       983      1004      1014      1024      1034      1044         
                                                                                                                        850|    873|             894|                                                                                     992|                                                 
                                                                                                                         866     878              904                                                                                     1004                                                 


Chain C from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.............hhhhh..eeeeee.........eeeee..eeeeeeeeeeeeeee.hhhhhhhhhhhhhhhhh......eeeeee....eehhhhhhhhh..................eeee..........eeeeeee...............hhhhhhhhhhh.........eeeee................hhhhhhhhhhhhh.eehhh.eee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ngf C  756 QPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRLYCVLPLNVVTLDIDFKFMEDIEKSEKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC 1053
                                   765       775       785       795       805       815       825       835       845    || 870   ||  884       894|      915       925       935       945       955       965       975       985      1005      1015      1025      1035      1045        
                                                                                                                        850|     874|            894|                                                                                     994|                                                
                                                                                                                         866      879             906                                                                                     1005                                                


Chain D from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee.............hhhhh..eeeeee.........eeeee..eeeeeeeeeeee....hhhhhhhhhhhhhhhhhh....eeeeee....eehhhhhhhhh.....................eeee..........eeeeeee...............hhhhhhhhh...........eeeee................hhhhhhhhhhhhhheehhh.eee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ngf D  756 QPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELKKSGFMLSLQMLELITRLHQYIFSHILRYCVLPLNVSTLDIDFKFMEDIEKSEKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC 1053
                                   765       775       785       795       805       815       825       835       845   ||  871 ||    885       903       913       923       933       943       953       963       973       983       993||    1013      1023      1033      1043      1053
                                                                                                                       849|    873|             894|                                                                                        994|                                                
                                                                                                                        866     878              903                                                                                        1005                                                


Chain E from PDB  Type:RNA  Length:17
                                                  
                4ngf E    1 UCGAAGGUCCUUCGUUU   17
                                    10       


Chain F from PDB  Type:RNA  Length:17
                                                  
                4ngf F    1 UCGAAGGUCCUUCGUUU   17
                                    10       


Chain G from PDB  Type:RNA  Length:17
                                                  
                4ngf G    1 UCGAAGGUCCUUCGUUU   17
                                    10       


Chain H from PDB  Type:RNA  Length:17
                                                  
                4ngf H    1 UCGAAGGUCCUUCGUUU   17
                                    10
   Legend:   → Mismatch (orange background)
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    → 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 4NGF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

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    Thr A:905 - Lys A:906   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        DICER_HUMAN | Q9UPY3: 2eb1 4ngb 4ngc 4ngd 4ngg 4nh3 4nh5 4nh6 4nha 4wyq

(-) Related Entries Specified in the PDB File

4ngb 4ngc 4ngd 4ngg 4nh3 4nh5 4nh6 4nha