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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF MATRIX PROTEIN 1 FROM INFLUENZA A VIRUS A/CROW/KYOTO/T1/2004(H5N1)
 
Authors :  S. Saijo, S. Kishishita, T. Uchikubo-Kamo, T. Terada, M. Shirouzu, H. I S. Yokoyama, Riken Structural Genomics/Proteomics Initiative
Date :  08 May 07  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Aiv-7M1, M1, Influenza A Virus, H5N1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Saijo, S. Kishishita, T. Uchikubo-Kamo, T. Terada, M. Shirouzu, H. Ito, T. Ito, S. Yokoyama
Crystal Structure Of Matrix Protein 1 From Influenza A Viru A/Crow/Kyoto/T1/2004(H5N1)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MATRIX PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: CELL-FREE PROTEIN SYNTHESIS
    Expression System Plasmid: PX070216-20
    Expression System Vector Type: PLASMID
    Gene: M1
    Organism Scientific: INFLUENZA A VIRUS
    Organism Taxid: 11320
    Strain: A/CROW/KYOTO/T1/2004(H5N1)
    Synonym: M1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Z16)

(-) Sites  (0, 0)

(no "Site" information available for 2Z16)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z16)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z16)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z16)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z16)

(-) 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:153
 aligned with A4PIH9_9INFA | A4PIH9 from UniProtKB/TrEMBL  Length:187

    Alignment length:156
                                                                                 1       10         11                                                                                  
                                     -         -         -         -         -   |     7  |      -   |    17        27        37        47        57        67        77        87      
         A4PIH9_9INFA     - -----------------------------------------------------LTVPSERGLQ----------RRRFVQNALNGNGDPNNMDRAVKLYKKLKREITFHGAKEVALSYSTGALASCMGLIYNRMGTVTTEVAFGLVCATCEQIADSQ  93
               SCOP domains d2z16a_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains 2z16A01 A:-2-79  [code=1.20.91.10, no name defined]                          2z16A0   2 A:80-157  [code=1.10.10.180, no name defined]                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhhh---hhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z16 A  -2 SSGMSLLTEVETYVLSIIPSGPLKAEIAQKLEDVFAGKNTDLEALMEWLKTRPILSPLTKGILGFVFTLTVPSRRRFVQNALN---DPNNMDRAVKLYKKLKREITFHGAKEVALSYSTGALASCMGLIYNRMGTVTTEVAFGLVCATCEQIADSQ 158
                                     7        17        27        37        47        57        67  ||    82  |   | 92       102       112       122       132       142       152      
                                                                                                   70|       85  89                                                                     
                                                                                                    76                                                                                  


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with A4PIH9_9INFA | A4PIH9 from UniProtKB/TrEMBL  Length:187

    Alignment length:160
                                                                                               1                                                                                            
                                     -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93
         A4PIH9_9INFA     - -------------------------------------------------------------------LTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYKKLKREITFHGAKEVALSYSTGALASCMGLIYNRMGTVTTEVAFGLVCATCEQIADSQ  93
               SCOP domains d2z16b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains 2z16B01 B:-1-79  [code=1.20.91.10, no name defined]                              2z16B02      B:80-157  [code=1.10.10.180, no name defin  ed]                  - CATH domains
           Pfam domains (1) -------------------------------------------------------------------Flu_M1   -2z16B01 B:6     6-157                                                             - Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------Flu_M1   -2z16B02 B:6     6-157                                                             - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhh...---..hhhhhhhhh.-----hhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhh.--..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z16 B  -1 SGMSLLTEVETYVLSIIPSGPLKAEIAQKLEDVFAGKNTDLEALMEWLKTRPILSPLTKGILGFVFTLTVPSE---QRRRFVQNALNG-----NMDRAVKLYKKLKREITFHGAKEVALSYSTGALASCMGLIYNR--TVTTEVAFGLVCATCEQIADSQ 158
                                     8        18        28        38        48        58        68  |   | 78       | -   |    98       108       118       128     | 138       148       158
                                                                                                   71  75         86    92                                       134  |                     
                                                                                                                                                                    137
   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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Flu_M1] (2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A4PIH9_9INFA | A4PIH9)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0039660    structural constituent of virion    The action of a molecule that contributes to the structural integrity of a virion.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

 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 2z16)
 
  Sites
(no "Sites" information available for 2z16)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2z16)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  2z16
    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
  A4PIH9_9INFA | A4PIH9
    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
  A4PIH9_9INFA | A4PIH9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2Z16)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2Z16)