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(-) Description

Title :  CRYSTAL STRUCTURE OF RNASE J COMPLEXED WITH RNA
 
Authors :  M. Lu, H. Zhang, Q. Xu, Y. Hua, Y. Zhao
Date :  29 Jan 15  (Deposition) - 16 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,D,E
Keywords :  Ribonuclease, Two-Metal-Ion, Dimerization, Manganese, Deinococcus Radiodurans, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhao, M. Lu, H. Zhang, J. Hu, C. Zhou, Q. Xu, A. M. U. H. Shah, H. Xu, L. Wang, Y. Hua
Structural Insights Into Catalysis And Dimerization Enhance Exonuclease Activity Of Rnase J
Nucleic Acids Res. V. 43 5550 2015
PubMed-ID: 25940620  |  Reference-DOI: 10.1093/NAR/GKV444

(-) Compounds

Molecule 1 - DR2417
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) ROSSETTA
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299
 
Molecule 2 - RNA (5'-D(UP*UP*UP*UP*UP*UP*U)-3')
    Chains: D, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MN2Ligand/IonMANGANESE (II) ION
3ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:84 , HIS A:86 , HIS A:153 , ASP A:175 , ZN A:602 , HOH D:107binding site for residue ZN A 601
2AC2SOFTWAREASP A:88 , HIS A:89 , HIS A:403 , ZN A:601 , U D:2 , HOH D:107binding site for residue ZN A 602
3AC3SOFTWAREGLY A:59 , ASP A:456binding site for residue MN A 603
4AC4SOFTWAREARG A:407 , HOH A:788 , HOH A:938 , HOH A:1063 , VAL B:354 , TYR B:370binding site for residue GOL A 604
5AC5SOFTWAREVAL A:354 , VAL A:358 , HOH A:777 , HOH A:816 , HOH A:885 , ARG B:407binding site for residue GOL A 605
6AC6SOFTWAREASP B:88 , HIS B:89 , HIS B:403 , ZN B:602 , U E:2binding site for residue ZN B 601
7AC7SOFTWAREHIS B:84 , HIS B:86 , HIS B:153 , ASP B:175 , ZN B:601binding site for residue ZN B 602
8AC8SOFTWAREGLY B:59 , ASP B:456binding site for residue MN B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Pro A:371 -Pro A:372
2His A:487 -Pro A:488
3Val A:558 -Asp A:559
4Pro B:371 -Pro B:372
5His B:487 -Pro B:488

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XWW)

(-) 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:545
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee........eeeeee..eeeee...............eeee.hhhhhhh...eeeeee...hhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhh....eeee.....eeee...eeeeeee........eeeeeee..eeeee..................hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..........hhhhhhhhhhh.eeeee........hhhhhhhh............eeee.......hhhhhhhhhhhhhhhh.eee.............hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh......ee......eeeeee..eeeeeee....eeeee..ee...hhhhhhhhhhhhhhheeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xww A  15 PAPTLEVIPLGGMGEIGKNITVFRYGDEIVVVDGGLAFPKAHQMGIDLIVPRIDYLLEHQDKIKGWILTHGHEDHIGGLPYIFARLPRVPVYGLPLTLALVREKLSEFGLQDVDLREVTYGDEVRFGQSFVAEFFCMTHSIPDNAGYILKTPVGDVLHTGDFKIDPDVGTGAGIVSDLERVEQAGKDGVLLLISDSTNAERPGHTPSEAEIARNLEEIIKGCRGRVFLTTFASQVYRIQNILDLAHRQGRRVVMEGRSMIKYAQAAQATGHMNPPEPFLTSEEVGELQDQQVLFVCTGSQGQPMAVLGRLAFGTHAKIALRRGDTVILSSNPIPGNEDAVNLIVNRLYEIGVDVVYPPTYRVHASGHASQEELATILNLTRPKFFLPWHGEPRHQINHAKLAQTLPRPPKRTLIAKNGDIVNLGPDEFRVSGTVAAGAVYVDGLGVGDVNDDVLLDRVNLSQEGLLILTAVLHPTPHVEVVARGFARPNRDLELQIRRVALEAVEQGLREKKRLEDVRDDMYGAVRRFTRKATGRNPVLIPMIVD 559
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554     


Chain B from PDB  Type:PROTEIN  Length:543
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee........eeeeee..eeeee...............eeee.hhhhhhh...eeeeee...hhhhhhhhhhhhh......eeehhhhhhhhhhhhhhh......eee.....eeee...eeeeeee........eeeeeee..eeeee..................hhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh..........hhhhhhhhhhh.eeeee........hhhhhhhh............eeee.......hhhhhhhhhhhhhhhh.eee.............hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh......ee......eeeeee..eeeeeee....eeeee..ee...hhhhhhhhhhhhhhheeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xww B  16 APTLEVIPLGGMGEIGKNITVFRYGDEIVVVDGGLAFPKAHQMGIDLIVPRIDYLLEHQDKIKGWILTHGHEDHIGGLPYIFARLPRVPVYGLPLTLALVREKLSEFGLQDVDLREVTYGDEVRFGQSFVAEFFCMTHSIPDNAGYILKTPVGDVLHTGDFKIDPDVGTGAGIVSDLERVEQAGKDGVLLLISDSTNAERPGHTPSEAEIARNLEEIIKGCRGRVFLTTFASQVYRIQNILDLAHRQGRRVVMEGRSMIKYAQAAQATGHMNPPEPFLTSEEVGELQDQQVLFVCTGSQGQPMAVLGRLAFGTHAKIALRRGDTVILSSNPIPGNEDAVNLIVNRLYEIGVDVVYPPTYRVHASGHASQEELATILNLTRPKFFLPWHGEPRHQINHAKLAQTLPRPPKRTLIAKNGDIVNLGPDEFRVSGTVAAGAVYVDGLGVGDVNDDVLLDRVNLSQEGLLILTAVLHPTPHVEVVARGFARPNRDLELQIRRVALEAVEQGLREKKRLEDVRDDMYGAVRRFTRKATGRNPVLIPMIV 558
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555   


Chain D from PDB  Type:DNA/RNA  Length:7
                                       
                 4xww D   0 UUUUUUU   6


Chain E from PDB  Type:DNA/RNA  Length:7
                                       
                 4xww E   0 UUUUUUU   6
   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 4XWW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His A:487 - Pro A:488   [ RasMol ]  
    His B:487 - Pro B:488   [ RasMol ]  
    Pro A:371 - Pro A:372   [ RasMol ]  
    Pro B:371 - Pro B:372   [ RasMol ]  
    Val A:558 - Asp A:559   [ RasMol ]  
 

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  4xww
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  H9CZL7_DEIRD | H9CZL7
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        H9CZL7_DEIRD | H9CZL7: 4xwt

(-) Related Entries Specified in the PDB File

4xwt