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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE III COMPLEXED WITH DOUBLE-STRANDED RNA AND CMP (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 :  2.85
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 - RNA10
    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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1C2Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:44 , GLU A:110 , HOH A:601 , C C:103 , G D:28 , HOH D:205BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP B:44 , GLU B:110 , HOH B:402 , G C:28 , C D:103 , HOH D:206BINDING SITE FOR RESIDUE MG B 301
3AC3SOFTWAREHOH A:606 , GLU B:64 , A C:2 , HOH C:204 , HOH C:205BINDING SITE FOR RESIDUE MG C 101
4AC4SOFTWAREA C:2 , A C:3BINDING SITE FOR RESIDUE MG C 102
5AC5SOFTWAREGLU A:40 , PHE A:41 , ASP A:44 , GLU A:110 , MG A:501 , GLU B:64 , SER B:68 , LYS B:71 , A C:2 , G C:26 , C C:27 , HOH C:204 , G D:28BINDING SITE FOR RESIDUE C C 103
6AC6SOFTWAREGLU A:64 , HOH B:403 , A D:2 , HOH D:207 , HOH D:208BINDING SITE FOR RESIDUE MG D 101
7AC7SOFTWAREA D:2 , A D:3BINDING SITE FOR RESIDUE MG D 102
8AC8SOFTWAREGLU A:64 , SER A:68 , LYS A:71 , GLU B:40 , PHE B:41 , ASP B:44 , GLU B:110 , MG B:301 , G C:28 , A D:2 , G D:26 , C D:27 , HOH D:206 , HOH D:207BINDING SITE FOR RESIDUE C D 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M2Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M2Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M2Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M2Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4M2Z)

(-) 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 ..hhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeeee......eeeeeeee..eee..ee.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m2z 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...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m2z 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
                                                           
                 4m2z C   2 AAGGUCAUUCGCAAGAGUGGCCUUGCG  28
                                    11        21       


Chain D from PDB  Type:RNA  Length:27
                                                           
                 4m2z D   2 AAGGUCAUUCGCAAGAGUGGCCUUGCG  28
                                    11        21
   Legend:   → Mismatch (orange background)
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    → 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 4M2Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M2Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M2Z)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  3.1.26.3
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 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 4m30

(-) Related Entries Specified in the PDB File

2nug CRYSTAL STRUCTURE OF RNASE III COMPLEXED WITH DOUBLE- STRANDED RNA (TYPE I CLEAVAGE)
4m30