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
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF NANOPARTICLE RELEASED FROM ENVELOPED PROTEIN NANOPARTICLE
 
Authors :  J. Votteler, C. Ogohara, S. Yi, Y. Hsia, U. Natterman, D. M. Belnap, N. P. W. I. Sundquist
Date :  02 Jul 16  (Deposition) - 07 Dec 16  (Release) - 11 Jan 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  5.70
Chains :  Asym. Unit :  B
Biol. Unit 1:  B  (60x)
Keywords :  Protein Design, Icosahedral Assemblies, Cell Transduction, Enveloped Viruses, Virus Assembly, Enveloped Protein, Nanoparticle, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Votteler, C. Ogohara, S. Yi, Y. Hsia, U. Nattermann, D. M. Belnap, N. P. King, W. I. Sundquist
Designed Proteins Induce The Formation Of Nanocage-Containing Extracellular Vesicles.
Nature V. 540 292 2016
PubMed-ID: 27919066  |  Reference-DOI: 10.1038/NATURE20607

(-) Compounds

Molecule 1 - EPN-01*
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Gene: TM_0066, GAG
    Organism Common: HIV-1
    Organism Scientific: THERMOTOGA MARITIMA, HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE BH10)
    Organism Taxid: 2336, 11678
    Strain: ISOLATE BH10
    Synonym: ENVELOPED PROTEIN NANOPARTICLE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : B
Biological Unit 1 (60x): B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5KP9)

(-) Sites  (0, 0)

(no "Site" information available for 5KP9)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:163 -B:201

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe B:129 -Pro B:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KP9)

(-) Exons   (0, 0)

(no "Exon" information available for 5KP9)

(-) 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 B from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhheeeee...hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhh...eee....hhhhhhhhhhhh.eee.ee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhh...eeehhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kp9 B   0 KMEELFKKHKIVAVLRANSVEEAKKKALAVFLGGVHLIEITFTVPDADTVIKELSFLKEMGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGSALVKGTPVEVAEKAKAFVEKIRGC 201
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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 5KP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KP9)

(-) Gene Ontology  (24, 24)

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 5kp9)
 
  Sites
(no "Sites" information available for 5kp9)
 
  Cis Peptide Bonds
    Phe B:129 - Pro B:130   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5kp9
    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
  GAG_HV1B1 | P03347
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q9WXS1_THEMA | Q9WXS1
    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
  GAG_HV1B1 | P03347
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q9WXS1_THEMA | Q9WXS1
    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
        GAG_HV1B1 | P03347: 2buo 5fjb
UniProtKB/TrEMBL
        Q9WXS1_THEMA | Q9WXS1: 1vlw 1wa3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KP9)