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 COMPLEXED WITH DOUBLE-STRANDED RNA AND AMP (TYPE II CLEAVAGE)
 
Authors :  J. Gan, Y. -H. Liang, G. X. Shaw, J. E. Tropea, D. S. Waugh, X. Ji
Date :  05 Aug 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rnase Iii, Hydrolase, Dsrna, Rna Binding, Rna Processing, Hydrolase- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Court, J. Gan, Y. H. Liang, G. X. Shaw, J. E. Tropea, N. Costantino, D. S. Waugh, X. Ji
Rnase Iii: Genetics And Function; Structure And Mechanism.
Annu. Rev. Genet. V. 47 405 2013
PubMed-ID: 24274754  |  Reference-DOI: 10.1146/ANNUREV-GENET-110711-155618

(-) Compounds

Molecule 1 - RIBONUCLEASE 3
    Chains: A, B
    EC Number: 3.1.26.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHPK1409
    Expression System Strain: BL21(DE3) CODONPLUS-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AQ_946, RNC
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: RIBONUCLEASE III, RNASE III
 
Molecule 2 - RNA12
    Chains: C, D
    Engineered: YES
    Other Details: CLEAVAGE PRODUCT OF A R1.1 RNA DERIVATIVE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1A2Ligand/IonADENOSINE-5'-MONOPHOSPHATE
2MG9Ligand/IonMAGNESIUM ION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:44 , GLU A:110 , MG A:502 , HOH A:601 , A C:103 , U D:28 , HOH D:201BINDING SITE FOR RESIDUE MG A 501
02AC2SOFTWAREGLU A:40 , GLU A:110 , MG A:501 , HOH A:602 , HOH A:603 , A C:103BINDING SITE FOR RESIDUE MG A 502
03AC3SOFTWAREASP B:44 , GLU B:110 , MG B:302 , HOH B:401 , U C:28 , HOH C:218 , A D:104BINDING SITE FOR RESIDUE MG B 301
04AC4SOFTWAREGLU B:40 , GLU B:110 , MG B:301 , HOH B:414 , A D:104BINDING SITE FOR RESIDUE MG B 302
05AC5SOFTWAREILE A:118 , VAL B:56 , GLN B:57 , LYS B:62BINDING SITE FOR RESIDUE MPD B 303
06AC6SOFTWAREHOH A:621 , HOH A:622 , HOH A:623 , A C:2 , HOH C:215 , HOH C:216BINDING SITE FOR RESIDUE MG C 101
07AC7SOFTWAREA C:2 , A C:3 , HOH C:213 , HOH C:214 , HOH C:217BINDING SITE FOR RESIDUE MG C 102
08AC8SOFTWAREGLU A:40 , PHE A:41 , ASP A:44 , GLU A:110 , MG A:501 , MG A:502 , HOH A:602 , HOH A:603 , HOH A:622 , SER B:68 , LYS B:71 , A C:2 , U C:26 , A C:27 , U D:28 , HOH D:201BINDING SITE FOR RESIDUE A C 103
09AC9SOFTWAREGLU A:64 , HOH A:624 , HOH B:415 , A D:2 , HOH D:209 , HOH D:211 , HOH D:212BINDING SITE FOR RESIDUE MG D 101
10BC1SOFTWAREA D:2 , A D:3 , HOH D:204 , HOH D:210BINDING SITE FOR RESIDUE MG D 102
11BC2SOFTWAREC D:23BINDING SITE FOR RESIDUE MG D 103
12BC3SOFTWAREGLU A:64 , SER A:68 , LYS A:71 , GLU B:40 , PHE B:41 , ASP B:44 , GLU B:110 , MG B:301 , MG B:302 , HOH B:414 , U C:28 , HOH C:218 , A D:2 , U D:26 , A D:27 , HOH D:211BINDING SITE FOR RESIDUE A D 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M30)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M30)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M30)

(-) Exons   (0, 0)

(no "Exon" information available for 4M30)

(-) 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
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m30 A   2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEESE 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m30 B   3 MLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        


Chain C from PDB  Type:RNA  Length:27
                                                           
                 4m30 C   2 AAGGUCAUUCGCAAGAGUGGCCUUUAU  28
                                    11        21       


Chain D from PDB  Type:RNA  Length:27
                                                           
                 4m30 D   2 AAGGUCAUUCGCAAGAGUGGCCUUUAU  28
                                    11        21
   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 4M30)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M30)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    A  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4m30)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4m30
    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
  RNC_AQUAE | O67082
    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)
  3.1.26.3
    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
  RNC_AQUAE | O67082
    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
        RNC_AQUAE | O67082: 1i4s 1jfz 1rc5 1rc7 1yyk 1yyo 1yyw 1yz9 2ez6 2nue 2nuf 2nug 4m2z

(-) Related Entries Specified in the PDB File

2nug CRYSTAL STRUCTURE OF RNASE III COMPLEXED WITH DOUBLE- STRANDED RNA (TYPE I CLEAVAGE)
4m2z