Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE III MUTANT E110K FROM AQUIFEX AEOLICUS COMPLEXED WITH DOUBLE-STRANDED RNA AT 2.9-ANGSTROM RESOLUTION
 
Authors :  J. Gan, J. E. Tropea, B. P. Austin, D. L. Court, D. S. Waugh, X. Ji
Date :  25 Feb 05  (Deposition) - 22 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Ribonuclease Iii, Double-Stranded Rna, Rna Interference, Endonucleolytic Cleavage, Hydrolase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Gan, J. E. Tropea, B. P. Austin, D. L. Court, D. S. Waugh, X. Ji
Intermediate States Of Ribonuclease Iii In Complex With Double-Stranded Rna
Structure V. 13 1435 2005
PubMed-ID: 16216575  |  Reference-DOI: 10.1016/J.STR.2005.06.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*G)-3'
    ChainsC, D, E, F
    EngineeredYES
    SyntheticYES
 
Molecule 2 - RIBONUCLEASE III
    ChainsA, B
    EC Number3.1.26.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHPK1409
    Expression System StrainBL21(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRNC
    MutationYES
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid63363
    SynonymRNASE III

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC E:3 , G E:4 , A E:5BINDING SITE FOR RESIDUE TRS E 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YYO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YYO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YYO)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_3_2PS50142 Ribonuclease III family domain profile.RNC_AQUAE4-121
 
  2A:4-121
B:4-121
2RNASE_3_1PS00517 Ribonuclease III family signature.RNC_AQUAE37-45
 
  2A:37-45
B:37-45
3DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RNC_AQUAE151-219
 
  2A:151-219
B:151-219

(-) Exons   (0, 0)

(no "Exon" information available for 1YYO)

(-) Sequences/Alignments

Asymmetric/Biological 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:220
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
            RNC_AQUAE     1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
               SCOP domains d1yyoa1 A:1-150 RNase III endonuclease catalytic domain                                                                                               d1yyoa2 A:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains 1yyoA01 A:1-149  [code=1.10.1520.10, no name defined]                                                                                                1yyoA02 A:150-220  [code=3.30.160.20, no name defined]                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh....hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---RNASE_3_2  PDB: A:4-121 UniProt: 4-121                                                                                -----------------------------DS_RBD  PDB: A:151-219 UniProt: 151-219                              - PROSITE (1)
                PROSITE (2) ------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yyo A   1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFKALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
            RNC_AQUAE     2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
               SCOP domains d1yyob1 B:2-150 RNase III endonuclease catalytic domain                                                                                              d1yyob2 B:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains 1yyoB01 B:2-149  [code=1.10.1520.10, no name defined]                                                                                               1yyoB02 B:150-220  [code=3.30.160.20, no name defined]                  CATH domains
           Pfam domains (1) -----------------------------------Ribonuclease_3-1yyoB03 B:37-121                                                      ------------------------------dsrm-1yyoB01 B:152-217                                            --- Pfam domains (1)
           Pfam domains (2) -----------------------------------Ribonuclease_3-1yyoB04 B:37-121                                                      ------------------------------dsrm-1yyoB02 B:152-217                                            --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhh....hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....eeeee........eeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --RNASE_3_2  PDB: B:4-121 UniProt: 4-121                                                                                -----------------------------DS_RBD  PDB: B:151-219 UniProt: 151-219                              - PROSITE (1)
                PROSITE (2) -----------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yyo B   2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFKALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         

Chain C from PDB  Type:RNA  Length:12
                                            
                 1yyo C   1 CGCGAAUUCGCG  12
                                    10  

Chain D from PDB  Type:RNA  Length:12
                                            
                 1yyo D  13 CGCGAAUUCGCG  24
                                    22  

Chain E from PDB  Type:RNA  Length:12
                                            
                 1yyo E   1 CGCGAAUUCGCG  12
                                    10  

Chain F from PDB  Type:RNA  Length:12
                                            
                 1yyo F  13 CGCGAAUUCGCG  24
                                    22  

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: DSRM (45)
(-)
Family: dsrm (27)
1adsrm-1yyoB01B:152-217
1bdsrm-1yyoB02B:152-217

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RNC_AQUAE | O67082)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004525    ribonuclease III activity    Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0016075    rRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yyo)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1yyo
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RNC_AQUAE | O67082
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.26.3
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RNC_AQUAE | O67082
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RNC_AQUAE | O670821i4s 1jfz 1rc5 1rc7 1yyk 1yyw 1yz9 2ez6 2nue 2nuf 2nug 4m2z 4m30

(-) Related Entries Specified in the PDB File

1i4s THE CRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1jfz CRYSTAL STRUCTURE OF A MN(II)COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1o0w THE CRYSTAL STRUCTURE OF RNASE III FROM THERMOTOGA MARITIMA
1rc5 THE CRYSTAL STRUCTURE OF A MG(II) COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1rc7 CRYSTAL STRUCTURE OF RNASE III MUTANT E110K FROM AQUIFEX AEOLICUS COMPLEXED WITH DOUBLE-STRANDED RNA
1yyk THE SAME PROTEIN AT 2.5-ANGSTROM RESOLUTION
1yyw THE SAME PROTEIN AT 2.8-ANGSTROM RESOLUTION
1yz9 THE SAME PROTEIN WITH MUTANT E110Q