Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF HUMAN DICER PLATFORM-PAZ-CONNECTOR HELIX CASSETTE IN COMPLEX WITH 16-MER SIRNA HAVING 5'-P AND UU-3' ENDS (3.4 ANGSTROM RESOLUTION)
 
Authors :  D. K. Simanshu, Y. Tian, J. -B Ma, D. J. Patel
Date :  04 Nov 13  (Deposition) - 05 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
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
    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*UP*UP*GP*GP*CP*CP*AP*AP*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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MSE-1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4NHA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NHA)

(-) 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:234
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeee.........hhhhh..eeee..........eee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhh.......eeee......hhhhhhhhh..............hhhhh..eeee.hhh......eeeeeee...............hhhhhhhhhhh.........eeeeee............eehhh.eeee..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4nha A  760 LYVIGmVLTTPLPDELRKLYPPEDTTRCFGILTAKPIPQIPVYTRSGEVTISIELKKSGFmLSLQmLELITRLHQYIFSHILRLSAYCVLPLNVTLDIDFKFmEDIEKSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPKQILVPELCAIHPIPASLWRKAVCLPSILYRLHC 1053
                                 | 769     ||783       793       803|      816       826|    | 836       846   ||  869   ||  884  |    902       912       922       932       942       952       962       972       982       992|     1029      1039      1049    
                                 |       775|                    803|                 827-MSE|               850|      873|     887-MSE93|                                                                                       992|                                 
                               765-MSE    780                     807                      832-MSE            864       879            902                                                                                       1020                                 


Chain B from PDB  Type:RNA  Length:16
                                                 
                4nha B    1 GCGUUGGCCAACGCUU   16
                                    10
   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 4NHA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (47, 47)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4nha)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4nha)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4nha
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DICER_HUMAN | Q9UPY3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.26.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DICER_HUMAN | Q9UPY3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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