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(-) Description

Title :  STRUCTURE OF HUMAN DICER PLATFORM-PAZ-CONNECTOR HELIX CASSETTE IN COMPLEX WITH 13-MER SIRNA HAVING 5'-A AND UU-3' ENDS (2.6 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 :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (2x)
Biol. Unit 2:  A,B  (2x)
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
    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
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HELICASE WITH RNASE MOTIF, HELICASE MOI
 
Molecule 2 - 5'-R(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
    Chains: B
    Engineered: YES
    Other Details: SIRNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A (1x)B (2x)
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:778 , ARG A:811 , HIS A:982 , SER A:984 , ARG A:986BINDING SITE FOR RESIDUE PO4 A 1101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4NGG)

(-) 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    
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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:267
                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee.............hhhhh..eeeeee.........eeeee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhhhh......eeeeeee.....eeehhhhhhhhhhhhh.................hhhhhh..eeee..........eeeeeee...............hhhhhhhhhhh.........eeeeee............hhhhhhhhhhheehhh.eee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ngg A  756 QPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELAASGFMLSLQMLELITRLHQYIFSHILRLEYCVLPLNVVNDSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC 1053
                                   765       775       785       795       805       815       825       835       845     ||869      |880       890       900       910       920       930       940       950       960       970       980       990  ||  1016      1026      1036      1046       
                                                                                                                         851|       876|                                                                                                                993|                                           
                                                                                                                          866        878                                                                                                                1010                                           


Chain B from PDB  Type:RNA  Length:13
                                              
                4ngg B    1 AGCGAAUUCGCUU   13
                                    10
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NGG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

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