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(-) Description

Title :  STRUCTURE OF HUMAN DICER PLATFORM-PAZ-CONNECTOR HELIX CASSETTE IN COMPLEX WITH 12-MER SIRNA HAVING 5'-P AND UU-3' ENDS (1.95 ANGSTROM RESOLUTION)
 
Authors :  Y. Tian, D. K. Simanshu, D. J. Patel
Date :  01 Nov 13  (Deposition) - 05 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
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(P*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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:778 , ARG A:780 , ARG A:811 , HIS A:982 , ARG A:993BINDING SITE FOR RESIDUE SO4 A 1101
2AC2SOFTWAREILE A:899 , ARG A:925 , TYR A:926 , PHE A:929 , PEG A:1103BINDING SITE FOR RESIDUE SO4 A 1102
3AC3SOFTWARETYR A:926 , ARG A:927 , ASN A:928 , PHE A:929 , TYR A:966 , SO4 A:1102 , PEG A:1104 , HOH A:1355BINDING SITE FOR RESIDUE PEG A 1103
4AC4SOFTWAREARG A:927 , ASN A:928 , TYR A:966 , ASN A:967 , PEG A:1103 , G B:1 , C B:10 , U B:11BINDING SITE FOR RESIDUE PEG A 1104

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NGD)

(-) 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:280
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee.hhhhh.......hhhhh..eeeeee.........eeeee..eeeeeeeeeeeeee..hhhhhhhhhhhhhhhhhh...........eeeeeee....eeehhhhhhhhhhh...................hhhhhh..eeee..........eeeeeee...............hhhhhhhhhhh.........eeeeee...............hhhhhhhhhhhhhhhhheehhh.eee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ngd A  756 QPCYLYVIGMVLTTPLPDELNFRRRKLYPPEDTTRCFGILTAKPIPQIPHFPVYTRSGEVTISIELAASGFMLSLQMLELITRLHQYIFSHILRLEKPALAYCVLPLNVVSSTLDIDFKFMEDIEKSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLPLSSAEKRKAKWESLQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC 1053
                                   765       775       785       795       805       815       825       835       845       855|      874|      886       896       906       916       926       936       946       956       966       976       986      1003      1013      1023      1033      1043      1053
                                                                                                                             855|      874|                                                                                                                  994|                                                   
                                                                                                                              865       877                                                                                                                  1002                                                   


Chain B from PDB  Type:RNA  Length:12
                                             
                4ngd B    1 GCGAAUUCGCUU   12
                                    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 4NGD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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