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 :  STRUCTURAL BASIS FOR CA2+-MEDIATED INTERACTION OF THE PERFORIN C2 DOMAIN WITH LIPID MEMBRANES
 
Authors :  P. J. Conroy, H. Yagi, J. C. Whisstock, R. S. Norton
Date :  09 Feb 15  (Deposition) - 02 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym./Biol. Unit :  A
Keywords :  Perforin, C2 Domain, Calcium Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yagi, P. J. Conroy, E. W. Leung, R. H. Law, J. A. Trapani, I. Voskoboinik, J. C. Whisstock, R. S. Norton
Structural Basis For Ca2+-Mediated Interaction Of The Perforin C2 Domain With Lipid Membranes.
J. Biol. Chem. V. 290 25213 2015
PubMed-ID: 26306037  |  Reference-DOI: 10.1074/JBC.M115.668384

(-) Compounds

Molecule 1 - PERFORIN-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOMB3X
    Expression System Strain: TOP10F`
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C2 DOMAIN (UNP RESIDUES 410-535)
    Gene: PRF1, PFP
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: P1,CYTOLYSIN,LYMPHOCYTE PORE-FORMING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:429 , ASP A:435 , ASP A:483 , ALA A:484 , ASP A:485 , CA A:604 , HOH A:705binding site for residue CA A 601
2AC2SOFTWAREASP A:485 , ASP A:489 , ASP A:491 , HOH A:707 , HOH A:718binding site for residue CA A 602
3AC3SOFTWAREASP A:429 , THR A:432 , ALA A:433 , ASP A:435 , ASN A:454 , GLU A:467binding site for residue CA A 603
4AC4SOFTWAREGLY A:428 , ASP A:429 , ASP A:483 , ASP A:485 , ASP A:491 , CA A:601 , HOH A:723 , HOH A:752binding site for residue CA A 604
5AC5SOFTWAREASP A:485 , ALA A:488 , ASP A:490 , HOH A:714 , HOH A:761binding site for residue CA A 605

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:496 -A:509
2A:524 -A:533

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Y1T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y1T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y1T)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y1T)

(-) 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:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeee...........eeeeeee..eeee..........ee...eeeeeee......eeeeeee.......eeeeeeee....eeeeeeee....eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y1t A 410 QRGLAHLVVSNFRAEHLAGDATTATDAYLKVFFGGQEFRTGVVWNNNNPRWTDKMDFENVLLSTGGPLRVQVWDADAGADDDLLGSCDRSPHSGFHEVTCELNHGRVKFSYHAKCLPHLTGGTCLE 535
                                   419       429       439       449       459       469       479       489       499       509       519       529
   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 4Y1T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y1T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y1T)

(-) Gene Ontology  (17, 17)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4y1t)
 

(-) 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
  4y1t
    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
  PERF_MOUSE | P10820
    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
  PERF_MOUSE | P10820
    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
        PERF_MOUSE | P10820: 3nsj 4y1s

(-) Related Entries Specified in the PDB File

4y1s