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(-) Description

Title :  CRYSTAL STRUCTURE OF PREFUSION-STABILIZED RSV F SINGLE-CHAIN 9-10 DS-CAV1 A149C-Y458C, S46G-E92D-S215P-K465Q VARIANT.
 
Authors :  M. G. Joyce, B. Zhang, J. R. Mascola, P. D. Kwong
Date :  24 May 16  (Deposition) - 17 Aug 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.92
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 26-103 AND RESIDUES 145-509 LINKED VIA LINKER RESIDUES GS
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS A (STRAIN A2)
    Organism Taxid: 11259
    Strain: A2
    Synonym: PROTEIN F,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  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO41Ligand/IonPHOSPHATE ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO43Ligand/IonPHOSPHATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU F:60 , ASP F:194binding site for residue ZN F 601
2AC2SOFTWAREHIS F:317 , HOH F:719 , HOH F:722binding site for residue ZN F 602
3AC3SOFTWARELYS F:176 , ASP F:263binding site for residue EDO F 603
4AC4SOFTWAREASP F:310binding site for residue EDO F 604
5AC5SOFTWAREGLU F:82 , LYS F:85 , GLN F:224 , GLN F:225binding site for residue PO4 F 605
6AC6SOFTWAREASN F:27binding site for Mono-Saccharide NAG F 606 bound to ASN F 27
7AC7SOFTWAREASN F:70binding site for Mono-Saccharide NAG F 607 bound to ASN F 70

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1F:37 -F:439
2F:69 -F:212
3F:149 -F:458
4F:155 -F:290
5F:313 -F:343
6F:322 -F:333
7F:358 -F:367
8F:382 -F:393
9F:416 -F:422

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr F:245 -Pro F:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K6I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K6I)

(-) Exons   (0, 0)

(no "Exon" information available for 5K6I)

(-) 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:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eeeeeeeeeeee.eeeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhh....eeeee.....eeeeeeeeehhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.eeeeeee...eeeeeeeeee..eeeeeeeeeee..ee..........eeee...eeeeee..eeeee.hhh.eeee..eeeee.hhheeehhhhhhhh..........eeeee.....eeee...eeeeee.....eeeee...eeeee...eeeeee.....eeee..eeee......eeeee...hhhhhh...........eehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k6i F  26 QNITEEFYQSTCSAVSKGYLGALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTDLQLLMQSTPATGSGSAICSGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSIPNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSRTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYCVNKQEGQSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKS 509
                                    35        45        55        65        75        85        95       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504     
                                                                                                       103|                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                        143
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  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 5K6I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K6I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K6I)

(-) Gene Ontology  (12, 12)

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 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 5k6b 5k6c 5k6f 5k6g 5k6h 5toj 5tok 5tpn 5u68 5udc

(-) Related Entries Specified in the PDB File

5k6b 5k6c 5k6f 5k6g 5k6h