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(-) Description

Title :  LEANYER ORTHOBUNYAVIRUS NUCLEOPROTEIN-SSDNA COMPLEX
 
Authors :  F. Niu, N. Shaw, Y. Wang, L. Jiao, W. Ding, X. Li, P. Zhu, H. Upur, S. Ouyang Z. J. Liu
Date :  01 Feb 13  (Deposition) - 10 Apr 13  (Release) - 05 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C,D,H,I
Keywords :  Protein-Dna Complex, Nucleic Acids Binding Protein, Nucleocapsid Protein, Viral Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Niu, N. Shaw, Y. E. Wang, L. Jiao, W. Ding, X. Li, P. Zhu, H. Upur, S. Ouyang, G. Cheng, Z. J. Liu
Structure Of The Leanyer Orthobunyavirus Nucleoprotein-Rna Complex Reveals Unique Architecture For Rna Encapsidation.
Proc. Natl. Acad. Sci. Usa V. 110 9054 2013
PubMed-ID: 23569220  |  Reference-DOI: 10.1073/PNAS.1300035110

(-) Compounds

Molecule 1 - NUCLEOCAPSID
    Chains: D, A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: LEANYER VIRUS
    Organism Taxid: 999729
 
Molecule 2 - DNA (5'- D(P*AP*CP*CP*AP*AP*AP*CP*AP*AP*CP*CP*CP*AP*CP*CP*CP*A)-3')
    Chains: H, I
    Engineered: YES
    Other Details: THIS SEQUENCE HAS BEEN DESIGNED AND THE SSDNA WAS SYNTHESISED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4J1J)

(-) Sites  (0, 0)

(no "Site" information available for 4J1J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J1J)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asp D:6 -Phe D:7
2Ser D:234 -Val D:235
3Thr A:3 -Gly A:4
4Ala B:14 -Ala B:15
5Ala C:14 -Ala C:15
6Ala C:218 -Gly C:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J1J)

(-) Exons   (0, 0)

(no "Exon" information available for 4J1J)

(-) 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:233
                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhh.hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1j A   3 TGPDFIYDDRPAAVSSTFNPEKGYMDFITAYGKNINADNVRIFFLNHKKAKDSLKGSPKVEVDLQFGTLRVKVVNNHNPRNRDNPVADNAITLHRLSGYLAKWCFDEIDHGQIEEAEVKSKVVIPLAEAKGCKWGDGVALYLAFAPGAEMFLKDFEFYPLAIDIQRVVKDGMDITFMRKVLKQRYGTKTADDWMISEVTAIQSAVKVVAKLPWAKAGFTAAAKNFLAKFNISV 235
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232   


Chain B from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1j B   5 PDFIYDDRPAAVSSTFNPEKGYMDFITAYGKNINADNVRIFFLNHKKAKDSLKGSPKVEVDLQFGTLRVKVVNNHNPRNRDNPVADNAITLHRLSGYLAKWCFDEIDHGQIEEAEVKSKVVIPLAEAKGCKWGDGVALYLAFAPGAEMFLKDFEFYPLAIDIQRVVKDGMDITFMRKVLKQRYGTKTADDWMISEVTAIQSAVKVVAKLPWAKAGFTAAAKNFLAKFNISV 235
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234 


Chain C from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j1j C   2 STGPDFIYDDRPAAVSSTFNPEKGYMDFITAYGKNINADNVRIFFLNHKKAKDSLKGSPKVEVDLQFGTLRVKVVNNHNPRNRDNPVADNAITLHRLSGYLAKWCFDEIDHGQIEEAEVKSKVVIPLAEAKGCKWGDGVALYLAFAPGAEMFLKDFEFYPLAIDIQRVVKDGMDITFMRKVLKQRYGTKTADDWMISEVTAIQSAVKVVAKLPWAKAGFTAAAKNFLAKFNISV 235
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231    


Chain D from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j1j D   6 DFIYDDRPAAVSSTFNPEKGYMDFITAYGKNINADNVRIFFLNHKKAKDSLKGSPKVEVDLQFGTLRVKVVNNHNPRNRDNPVADNAITLHRLSGYLAKWCFDEIDHGQIEEAEVKSKVVIPLAEAKGCKWGDGVALYLAFAPGAEMFLKDFEFYPLAIDIQRVVKDGMDITFMRKVLKQRYGTKTADDWMISEVTAIQSAVKVVAKLPWAKAGFTAAAKNFLAKFNISV 235
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235


Chain H from PDB  Type:DNA  Length:17
                                                 
                 4j1j H   1 ACCAAACAACCCACCCA  17
                                    10       


Chain I from PDB  Type:DNA  Length:17
                                                 
                 4j1j I   1 ACCAAACAACCCACCCA  17
                                    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 4J1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J1J)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:14 - Ala B:15   [ RasMol ]  
    Ala C:14 - Ala C:15   [ RasMol ]  
    Ala C:218 - Gly C:219   [ RasMol ]  
    Asp D:6 - Phe D:7   [ RasMol ]  
    Ser D:234 - Val D:235   [ RasMol ]  
    Thr A:3 - Gly A:4   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        F2WAD7_9VIRU | F2WAD7: 4j1g

(-) Related Entries Specified in the PDB File

4j1g