Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PREFUSION-STABILIZED RSV F SINGLE-CHAIN 9 DS-CAV1 VARIANT.
 
Authors :  M. G. Joyce, B. Zhang, E. J. Rundlet, J. R. Mascola, P. D. Kwong
Date :  24 May 16  (Deposition) - 31 Aug 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym. Unit :  F
Biol. Unit 1:  F  (3x)
Keywords :  Respiratory Syncytial Virus, Prefusion, Vaccine, Stabilized, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Joyce, B. Zhang, L. Ou, M. Chen, G. Y. Chuang, A. Druz, W. P. Kong, Y. T. Lai, E. J. Rundlet, Y. Tsybovsky, Y. Yang, I. S. Georgiev, M. Guttman, C. R. Lees, M. Pancera, M. Sastry, C. Soto, G. B. Stewart-Jones, P. V. Thomas, J. G. Van Galen, U. Baxa, K. K. Lee, J. R. Mascola, B. S. Graham, P. D. Kwong
Iterative Structure-Based Improvement Of A Fusion-Glycoprotein Vaccine Against Rsv.
Nat. Struct. Mol. Biol. V. 23 811 2016
PubMed-ID: 27478931  |  Reference-DOI: 10.1038/NSMB.3267

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F0
    Chains: F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 26-105 LINKED TO RESIDUES 145-509 VIA LINKER RESIDUES GS
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS A
    Organism Taxid: 11259
    Other Details: RSV F SINGLE-CHAIN 9 DS-CAV1VARIANT
    Strain: A2
    Synonym: PROTEIN F

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : F
Biological Unit 1 (3x): F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2SO412Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG F:235binding site for residue SO4 F 1002
2AC2SOFTWAREASP F:338 , ARG F:339 , HOH F:1101binding site for residue SO4 F 1003
3AC3SOFTWAREASN F:277 , ARG F:364binding site for residue SO4 F 1004
4AC4SOFTWARELYS F:498binding site for residue SO4 F 1005
5AC5SOFTWAREASN F:27binding site for Mono-Saccharide NAG F 1001 bound to ASN F 27

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1F:37 -F:439
2F:69 -F:212
3F:155 -F:290
4F:313 -F:343
5F:322 -F:333
6F:358 -F:367
7F:382 -F:393
8F:416 -F:422

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Thr F:100 -Pro F:101
2Glu F:161 -Gly F:162
3Thr F:245 -Pro F:246
4Lys F:327 -Glu F:328

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K6B)

(-) Exons   (0, 0)

(no "Exon" information available for 5K6B)

(-) 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 F from PDB  Type:PROTEIN  Length:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeeeeeeeeeeeeeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhh...hhhhhhhhh.....eeeee.....eeeeeeeeehhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...ee........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeeeeeeeeeeeeeeeee..ee..........eeee...eeeeee..eeeee......eee..eeeee.hhheeehhhhhhhhhh........eeeee.....eeee...eeeeee.....eeeee...eeeee...eeeeee.....eeee..eeee......eeeee...hhhhhh...........eehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k6b F  26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNGSGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSRTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLA 504
                                    35        45        55        65        75        85        95       105|      152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502  
                                                                                                         105|                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                          143
   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 5K6B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K6B)

(-) Gene Ontology  (12, 12)

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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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
    Glu F:161 - Gly F:162   [ RasMol ]  
    Lys F:327 - Glu F:328   [ RasMol ]  
    Thr F:100 - Pro F:101   [ RasMol ]  
    Thr F:245 - Pro F:246   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  5k6b
    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
  FUS_HRSVA | P03420
    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
  FUS_HRSVA | P03420
    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
        FUS_HRSVA | P03420: 2mdp 3ixt 3kpe 3o41 3o45 3rki 3rrr 3rrt 4ccf 4jhw 4mmq 4mmr 4mms 4mmt 4mmu 4mmv 4zyp 5c69 5c6b 5ea3 5ea4 5ea5 5ea6 5ea7 5ea8 5j3d 5k6c 5k6f 5k6g 5k6h 5k6i 5toj 5tok 5tpn 5u68 5udc

(-) Related Entries Specified in the PDB File

5k6c 5k6f 5k6g 5k6h 5k6i