Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  HEXAMERIC CRYSTAL STRUCTURE OF SCHMALLENBERG VIRUS NUCLEOPROTEIN
 
Authors :  H. Dong, C. Dong
Date :  13 Dec 12  (Deposition) - 24 Apr 13  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.21
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Nucleoprotein, Protects Genomic Rna, Rna Replication And Transcription, Sbv Nucleoprotein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Dong, P. Li, R. M. Elliott, C. Dong
Structure Of Schmallenberg Orthobunyavirus Nucleoprotein Suggests A Novel Mechanism Of Genome Encapsidation
J. Virol. V. 87 5593 2013
PubMed-ID: 23468499  |  Reference-DOI: 10.1128/JVI.00223-13

(-) Compounds

Molecule 1 - NUCLEOCAPSID PROTEIN
    Chains: B, A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PDST14
    Gene: N
    Organism Common: SBV
    Organism Scientific: SCHMALLENBERG VIRUS
    Organism Taxid: 1133363

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x): A  
Biological Unit 4 (1x):   C

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4IDX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Val B:69 -Lys B:70
2Ser B:216 -Gly B:217
3Arg A:13 -Asn A:14
4Thr A:17 -Phe A:18
5Phe A:18 -Asn A:19
6Val A:69 -Lys A:70
7Pro A:220 -Ala A:221
8Gln A:227 -Gln A:228
9Val C:69 -Lys C:70
10Met C:188 -Thr C:189
11Glu C:191 -Glu C:192
12Gln C:196 -Lys C:197
13Pro C:220 -Ala C:221
14Arg C:223 -Thr C:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IDX)

(-) Sequences/Alignments

Asymmetric 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee..eeee...................hhhhhhhhhhhhhhhhhh....hhhhhhhh..hhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.......hhhhhh..........................hhhhhh................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4idx A  11 PQRNAATFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQ 228
                                    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:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhh...........................hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4idx B  17 TFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTF 225
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         


Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhh...eee........eee.................hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhh......hhhhhh....................hhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4idx C  16 ATFNPEVGYVAFIGKYGQQLNFGVARVFFLNQKKAKMVLHKTAQPSVDLTFGGVKFTVVNNHFPQYVSNPVPDNAITLHRMSGYLARWIADTCKASVLKLAEASAQIVMPLAEVKGCTWADGYTMYLGFAPGAEMFLDAFDFYPLVIEMHRVLKDNMDVNFMKKVLRQRYGTMTAEEWMTQKITEIKAAFNSVGQLAWAKSGFSPAARTFLQQ 228
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
   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 4IDX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 4idx)
 
  Sites
(no "Sites" information available for 4idx)
 
  Cis Peptide Bonds
    Arg A:13 - Asn A:14   [ RasMol ]  
    Arg C:223 - Thr C:224   [ RasMol ]  
    Gln A:227 - Gln A:228   [ RasMol ]  
    Gln C:196 - Lys C:197   [ RasMol ]  
    Glu C:191 - Glu C:192   [ RasMol ]  
    Met C:188 - Thr C:189   [ RasMol ]  
    Phe A:18 - Asn A:19   [ RasMol ]  
    Pro A:220 - Ala A:221   [ RasMol ]  
    Pro C:220 - Ala C:221   [ RasMol ]  
    Ser B:216 - Gly B:217   [ RasMol ]  
    Thr A:17 - Phe A:18   [ RasMol ]  
    Val A:69 - Lys A:70   [ RasMol ]  
    Val B:69 - Lys B:70   [ RasMol ]  
    Val C:69 - Lys C:70   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  4idx
    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
  NCAP_SBVBH | H2AM13
    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)
  (no 'Enzyme Classificator' available)
    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
  NCAP_SBVBH | H2AM13
    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
        NCAP_SBVBH | H2AM13: 3zl9 4idu 4jng

(-) Related Entries Specified in the PDB File

4idu SBV NUCLEOPROTEIN HEXAMERIC FORM