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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RSV F GLYCOPROTEIN IN COMPLEX WITH THE NEUTRALIZING SINGLE-DOMAIN ANTIBODY F-VHH-L66
 
Authors :  M. S. A. Gilman, S. C. Kabeche, J. S. Mclellan
Date :  17 Oct 16  (Deposition) - 22 Feb 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Fusion, Nanobody, Immunoglobulin Fold, Complex, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Rossey, M. S. Gilman, S. C. Kabeche, K. Sedeyn, D. Wrapp, M. Kanekiyo M. Chen, V. Mas, J. Spitaels, J. A. Melero, B. S. Graham, B. Schepens, J. S. Mclellan, X. Saelens
Potent Single-Domain Antibodies That Arrest Respiratory Syncytial Virus Fusion Protein In Its Prefusion State.
Nat Commun V. 8 14158 2017
PubMed-ID: 28194013  |  Reference-DOI: 10.1038/NCOMMS14158

(-) Compounds

Molecule 1 - FUSION GLYCOPROTEIN F0, FIBRITIN CHIMERA
    Chains: A, B, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Mutation: YES
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS
    Organism Taxid: 11250
    Synonym: PROTEIN F
 
Molecule 2 - SINGLE-DOMAIN ANTIBODY F-VHH-L66
    Chains: D, E, F
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS GS115
    Expression System Taxid: 644223
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:183 , ASN B:426 , LYS B:427 , GLY B:446 , ASP B:448 , LYS B:461binding site for residue PO4 B 602
2AC2SOFTWAREASN A:500binding site for Mono-Saccharide NAG A 800 bound to ASN A 500
3AC3SOFTWAREASN B:500binding site for Mono-Saccharide NAG B 601 bound to ASN B 500
4AC4SOFTWAREASN C:500binding site for Mono-Saccharide NAG C 800 bound to ASN C 500

(-) SS Bonds  (30, 30)

Asymmetric/Biological Unit
No.Residues
1A:37 -A:439
2A:69 -A:212
3A:155 -A:290
4A:313 -A:343
5A:322 -A:333
6A:358 -A:367
7A:382 -A:393
8A:416 -A:422
9B:37 -B:439
10B:69 -B:212
11B:155 -B:290
12B:313 -B:343
13B:322 -B:333
14B:358 -B:367
15B:382 -B:393
16B:416 -B:422
17C:37 -C:439
18C:69 -C:212
19C:155 -C:290
20C:313 -C:343
21C:322 -C:333
22C:358 -C:367
23C:382 -C:393
24C:416 -C:422
25D:22 -D:92
26D:50 -D:100C
27E:22 -E:92
28E:50 -E:100C
29F:22 -F:92
30F:50 -F:100C

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:245 -Pro A:246
2Thr B:245 -Pro B:246
3Thr C:245 -Pro C:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TOK)

(-) 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 A from PDB  Type:PROTEIN  Length:478
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeeeeeeeee.eeeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeeeeeeehhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh...ee........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeeeee..eeeeeeeeeee..ee..........eeee...eeeeee..eeeee.hhhhheee..eeeee.hhheeehhhhhhhhhh........eeeee.....eeee...eeeeee.....eeeee...eeeee...eeeeee.....eeee..eeee......eeeee...hhhhhh...........eehhhhhhhhhhhhhhhhhhhhhhh...............eeee..eeee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tok A   27 NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLLSTFL  544
                                    36        46        56        66        76        86        96|      146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536        
                                                                                                96|                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                137                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:478
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeeeeeeeee.eeeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.....hhhhhhhhhhhh..hhhhhhhhhh....eeeee.....eeeeeeeeehhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...ee........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeeeee..eeeeeeeeeee..ee....hhhhh.eeee...eeeeee..eeeee.hhhhheee..eeeee.hhheeehhhhhhhhhh........eeeee.....eeee...eeeeee.....eeeee...eeeee...eeeeee.....eeee..eeee.......eeee...hhhhhh...........eehhhhhhhhhhhhhhhhhhhhhhhhhh............eeee..eeee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tok B   27 NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLLSTFL  544
                                    36        46        56        66        76        86        96|      146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536        
                                                                                                96|                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                137                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:478
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeeeeeeeeee.eeeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhh....eeeee.....eeeeeeeeehhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh...ee........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeeeeee..eeeeeeeeeee..ee....hhhhh.eeee...eeeeee..eeeee.hhhhheee..eeeee.hhheeehhhhhhhh..........eeeee.....eeee...eeeeee.....eeeee...eeeee...eeeeee.....eeee..eeee.......eeee...hhhhhh...........eehhhhhhhhhhhhhhhhhhhhhhh...............eeee..eeee.hhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5tok C   27 NITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLLSTFL  544
                                    36        46        56        66        76        86        96|      146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536        
                                                                                                96|                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                137                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..ee......eeeeeeee..hhh.eeeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee.hhh...hhhhh.ee...eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                5tok D    1 QVQLQESGGGLVQPGGSLRLSCAASGFTLDYYYIGWFRQAPGKEREGVSCISSSHGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATVAVAHFRGCGVDGMDYWGKGTQVTV  111
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108   
                                                                              52A                            82A||               100A|||||||           
                                                                                                              82B|                100B||||||           
                                                                                                               82C                 100C|||||           
                                                                                                                                    100D||||           
                                                                                                                                     100E|||           
                                                                                                                                      100F||           
                                                                                                                                       100G|           
                                                                                                                                        100H           


Chain E from PDB  Type:PROTEIN  Length:126
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee..hhh.eeeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee.hhh...hhhhh.ee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                5tok E    2 VQLQESGGGLVQPGGSLRLSCAASGFTLDYYYIGWFRQAPGKEREGVSCISSSHGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATVAVAHFRGCGVDGMDYWGKGTQVTVSSHH  115
                                    11        21        31        41        51 |      60        70        80  |||   87        97   |||100G|      109      
                                                                             52A                            82A||               100A|||||||               
                                                                                                             82B|                100B||||||               
                                                                                                              82C                 100C|||||               
                                                                                                                                   100D||||               
                                                                                                                                    100E|||               
                                                                                                                                     100F||               
                                                                                                                                      100G|               
                                                                                                                                       100H               


Chain F from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee..hhh.eeeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee.hhh...hhhhh.ee...eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                5tok F    1 QVQLQESGGGLVQPGGSLRLSCAASGFTLDYYYIGWFRQAPGKEREGVSCISSSHGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATVAVAHFRGCGVDGMDYWGKGTQVTV  111
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108   
                                                                              52A                            82A||               100A|||||||           
                                                                                                              82B|                100B||||||           
                                                                                                               82C                 100C|||||           
                                                                                                                                    100D||||           
                                                                                                                                     100E|||           
                                                                                                                                      100F||           
                                                                                                                                       100G|           
                                                                                                                                        100H
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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 5TOK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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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 5k6i 5toj 5tpn 5u68 5udc

(-) Related Entries Specified in the PDB File

5toj