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 THE ENDONUCLEASE FROM THE PA SUBUNIT OF INFLUENZA B VIRUS BOUND TO THE PB2 SUBUNIT NLS PEPTIDE
 
Authors :  D. Guilligay, S. Gaudon, S. Cusack
Date :  06 Nov 15  (Deposition) - 13 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Protein, Endonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Thierry, D. Guilligay, J. Kosinski, T. Bock, S. Gaudon, A. Round, A. Pflug, N. Hengrung, K. El Omari, F. Baudin, D. J. Hart, M. Beck, S. Cusack
Influenza Polymerase Can Adopt An Alternative Configuration Involving A Radical Repacking Of Pb2 Domains.
Mol. Cell V. 61 125 2016
PubMed-ID: 26711008  |  Reference-DOI: 10.1016/J.MOLCEL.2015.11.016

(-) Compounds

Molecule 1 - PA SUBUNIT OF INFLUENZA B POLYMERASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: RIL
    Expression System Vector Type: PLASMID
    Fragment: ENDONUCLEASE DOMAIN RESIDUES 1-197
    Organism Scientific: INFLUENZA B VIRUS
    Organism Taxid: 11520
    Strain: B/MEMPHIS/13/2003/
 
Molecule 2 - PB2 SUBUNIT OF INFLUENZA B POLYMERASE
    Chains: A
    Fragment: NLS PEPTIDE RESIDUES 742-770
    Organism Scientific: INFLUENZA B VIRUS
    Organism Taxid: 11520
    Strain: B/MEMPHIS/13/2003/
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:41 , ASP B:109 , GLU B:120 , VAL B:121 , MG B:1196 , HOH B:2023BINDING SITE FOR RESIDUE MG B1195
2AC2SOFTWAREHIS B:41 , GLU B:81 , ASP B:109 , MG B:1195 , HOH B:2023 , HOH B:2046 , HOH B:2048 , HOH B:2059BINDING SITE FOR RESIDUE MG B1196
3AC3SOFTWAREGLU B:23 , GLN B:67 , ARG B:85 , THR B:86 , HOH B:2018BINDING SITE FOR RESIDUE GOL B1197

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FML)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FML)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FML)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FML)

(-) Exons   (0, 0)

(no "Exon" information available for 5FML)

(-) 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:19
                                                   
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                 5fml A 747 LSNDISQGIKRQRMTVESM 765
                                   756         


Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....eeehhhhh.hhh.eee.eee....hhhhhhhhhhhhhhhh..........eee....eeeeeeee..hhhhhhhhhhhhhh...eeeeee....ee.......hhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fml B  -1 MAMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCYVISDMNFLDEEGKSYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFDYKTKRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEGKGRVLSRLTELQAELSLKNLWQVLIGEE 194
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   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 5FML)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FML)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FML)

(-) Gene Ontology  (10, 13)

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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fml)
 

(-) 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
  5fml
    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
  Q5V8X3_9INFB | Q5V8X3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q5V8Z9_9INFB | Q5V8Z9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q5V8X3_9INFB | Q5V8X3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q5V8Z9_9INFB | Q5V8Z9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5V8X3_9INFB | Q5V8X3: 4wrt 4wsa 5epi 5fmz 5m3j 5msg
        Q5V8Z9_9INFB | Q5V8Z9: 4wrt 4wsa 5epi 5fmz 5m3j 5msg

(-) Related Entries Specified in the PDB File

5fmm INFLUENZA POLYMERASE CAN ADOPT AN ALTERNATIVE CONFIGURATION INVOLVING A RADICAL REPACKING OF PB2 DOMAINS
5fmq INFLUENZA POLYMERASE CAN ADOPT AN ALTERNATIVE CONFIGURATION INVOLVING A RADICAL REPACKING OF PB2 DOMAINS