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 :  NATIVELY MEMBRANE-ANCHORED FULL-LENGTH HERPES SIMPLEX VIRUS 1 GLYCOPROTEIN B
 
Authors :  T. Zeev-Ben-Mordehai, D. Vasishtan, A. H. Duran, B. Vollmer, P. White, A. P. Pandurangan, C. A. Siebert, M. Topf, K. Grunewald
Date :  10 Mar 16  (Deposition) - 23 Mar 16  (Release) - 29 Jun 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  23.00
Chains :  Asym. Unit :  A,B,C  (4x)
Biol. Unit 1:  A,B,C  (1x)
Keywords :  Viral Protein, Membrane Fusion, Class Iii Fusogen, Pre-Fusion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zeev-Ben-Mordehai, D. Vasishtan, A. Hernandez Duran, B. Vollmer P. White, A. Prasad Pandurangan, C. A. Siebert, M. Topf, K. Grunewald
Two Distinct Trimeric Conformations Of Natively Membrane- Anchored Full-Length Herpes Simplex Virus 1 Glycoprotein B.
Proc. Natl. Acad. Sci. Usa V. 113 4176 2016
PubMed-ID: 27035968  |  Reference-DOI: 10.1073/PNAS.1523234113

(-) Compounds

Molecule 1 - ENVELOPE GLYCOPROTEIN B
    Chains: A, B, C
    Engineered: YES
    Expression System: MESOCRICETUS AURATUS
    Expression System Common: GOLDEN HAMSTER
    Expression System Plasmid: PPEP98
    Expression System Taxid: 10036
    Expression System Vector Type: PLASMID
    Fragment: DOMAINS I AND II
    Organism Common: HERPES SIMPLEX VIRUS TYPE 1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Synonym: GB, GB-1, GB1, GLYCOPROTEIN B

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit (4x): ABC
Biological Unit 1 (1x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5FZ2)

(-) Sites  (0, 0)

(no "Site" information available for 5FZ2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FZ2)

(-) Cis Peptide Bonds  (9, 18)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4Tyr A:282 -Pro A:283
21, 2, 3, 4Tyr B:282 -Pro B:283
31, 2, 3, 4Tyr C:282 -Pro C:283
42Val A:363 -Cys A:364
52Val B:363 -Cys B:364
62Val C:363 -Cys C:364
73Val A:357 -Pro A:358
83Val B:357 -Pro B:358
93Val C:357 -Pro C:358

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 5FZ2)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeeeeeeeeeeeeeeee....eeeeeeeeeeee.hhhhhhhh.....eee.eeeeee..eeeeee.hhh...eee.ee.........eee..............eeeeeeeeeeeeeeeeee......eee....ee..........hhhhh....hhh.eeeeeee..............eeeeeee....eeeeee.hhhhhh..eeeeeee..eeeeee..eeeeee....eeeee.....hhhhh..hhhhhhhhhhhhhhhhhhh....eee....eeee.....eeeeeeeee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fz2 A 142 YTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTLAELYVREHLREQSRKPP 477
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      


Chain B from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeeeeeeeeeeeeeeee....eeeeeeeeeeee.hhhhhhhh.....eee.eeeeee..eeeeee.hhh...eee.ee.........eee..............eeeeeeeeeeeeeeeeee......eee....ee..........hhhhh....hhh.eeeeeee..............eeeeeee....eeeeee.hhhhhh..eeeeeee..eeeeee..eeeeee....eeeee.....hhhhh..hhhhhhhhhhhhhhhhhhh....eee....eeee.....eeeeeeeee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fz2 B 142 YTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTLAELYVREHLREQSRKPP 477
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      


Chain C from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeeeeeeeeeeeeeeee....eeeeeeeeeeee.hhhhhhhh.....eee.eeeeee..eeeeee.hhh...eee.ee.........eee..............eeeeeeeeeeeeeeeeee......eee....ee..........hhhhh....hhh.eeeeeee..............eeeeeee....eeeeee.hhhhhh..eeeeeee..eeeeee..eeeeee....eeeee.....hhhhh..hhhhhhhhhhhhhhhhhhh....eee....eeee.....eeeeeeeee.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fz2 C 142 YTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRYSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTTYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYQANGGFLIAYQPLLSNTLAELYVREHLREQSRKPP 477
                                   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471
   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 5FZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FZ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FZ2)

(-) Gene Ontology  (14, 14)

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 5fz2)
 
  Sites
(no "Sites" information available for 5fz2)
 
  Cis Peptide Bonds
    Tyr A:282 - Pro A:283   [ RasMol ]  
    Tyr B:282 - Pro B:283   [ RasMol ]  
    Tyr C:282 - Pro C:283   [ RasMol ]  
    Val A:357 - Pro A:358   [ RasMol ]  
    Val A:363 - Cys A:364   [ RasMol ]  
    Val B:357 - Pro B:358   [ RasMol ]  
    Val B:363 - Cys B:364   [ RasMol ]  
    Val C:357 - Pro C:358   [ RasMol ]  
    Val C:363 - Cys C:364   [ 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
  5fz2
    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
  GB_HHV1K | P06437
    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
  GB_HHV1K | P06437
    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
        GB_HHV1K | P06437: 2gum 3nw8 3nwa 3nwd 3nwf 3wv0 4bom 4hsi 4l1r

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5FZ2)