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 :  SUB-TOMOGRAM AVERAGING OF LASSA VIRUS GLYCOPROTEIN SPIKE FROM VIRUS-LIKE PARTICLES AT PH 5
 
Authors :  S. Li, S. Zhaoyang, R. Pryce, M. L. Parsy, S. K. Fehling, K. Schlie, C. A. S W. Garten, T. A. Bowden, T. Strecker, J. T. Huiskonen
Date :  09 Jan 16  (Deposition) - 02 Mar 16  (Release) - 02 Mar 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  16.40
Chains :  Asym./Biol. Unit :  B
Keywords :  Cell Adhesion, Membrane Protein, Glycoprotein, Receptor Binding, Membrane Fusion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Li, Z. Sun, R. Pryce, M. Parsy, S. K. Fehling, K. Schlie, C. A. Siebert W. Garten, T. A. Bowden, T. Strecker, J. T. Huiskonen
Acidic Ph-Induced Conformations And Lamp1 Binding Of The Lassa Virus Glycoprotein Spike.
Plos Pathog. V. 12 5418 2016
PubMed-ID: 26849049  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1005418
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: RECEPTOR BINDING DOMAIN, UNP RESIDUES 75-237
    Organism Common: LASSA MAMMARENAVIRUS, LASV
    Organism Scientific: LASSA VIRUS
    Organism Taxid: 11622
    Strain: JOSIAH
    Synonym: GP1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:89 , ASN B:109 , SER B:171 , SER B:216 , GLN B:218 , HOH B:406BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 301 THROUGH NAG B 302 BOUND TO ASN B 109
2AC2SOFTWAREASN B:119BINDING SITE FOR MONO-SACCHARIDE NAG B 304 BOUND TO ASN B 119
3AC3SOFTWAREASN B:114 , HIS B:115 , LYS B:116 , MET B:153 , SER B:154 , ASN B:167 , TYR B:219BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B 305 THROUGH NAG B 306 BOUND TO ASN B 167
4AC4SOFTWARETHR B:101 , LEU B:103 , HIS B:131 , GLY B:160 , ASN B:224 , HOH B:404BINDING SITE FOR MONO-SACCHARIDE NAG B 303 BOUND TO ASN B 224

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1B:86 -B:231
2B:118 -B:155
3B:180 -B:212

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FT2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FT2)

(-) Exons   (0, 0)

(no "Exon" information available for 5FT2)

(-) 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 B from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee......eeeeeee.............hhhhhhhhhhhhhhhhhhh...........eeeeeee..eeeeeee....hhhhhhhh..hhhhhhhhhhhhhh.....eeee......eeee....eeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ft2 B  81 TMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPS 237
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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 5FT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FT2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FT2)

(-) Gene Ontology  (15, 15)

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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ft2)
 

(-) 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
  5ft2
    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
  GLYC_LASSJ | P08669
    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
  GLYC_LASSJ | P08669
    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
        GLYC_LASSJ | P08669: 4zjf 5vk2

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5FT2)