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(-) Description

Title :  CRYSTAL STRUCTURE OF RESPIRATORY SYNCYTIAL VIRUS FUSION GLYCOPROTEIN STABILIZED IN THE PREFUSION CONFORMATION BY HUMAN ANTIBODY D25
 
Authors :  J. S. Mclellan, M. Chen, S. Leung, K. W. Graepel, X. Du, Y. Yang, T. Zhou, U E. Yasuda, T. Beaumont, A. Kumar, K. Modjarrad, Z. Zheng, M. Zhao, N. Xi P. D. Kwong, B. S. Graham
Date :  05 Mar 13  (Deposition) - 01 May 13  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  F,H,L
Biol. Unit 1:  F,H,L  (3x)
Keywords :  Immunoglobulin; Type I Fusion Protein, Membrane Fusion, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Mclellan, M. Chen, S. Leung, K. W. Graepel, X. Du, Y. Yang, T. Zhou, U. Baxa, E. Yasuda, T. Beaumont, A. Kumar, K. Modjarrad, Z. Zheng, M. Zhao, N. Xia, P. D. Kwong, B. S. Graham
Structure Of Rsv Fusion Glycoprotein Trimer Bound To A Prefusion-Specific Neutralizing Antibody.
Science V. 340 1113 2013
PubMed-ID: 23618766  |  Reference-DOI: 10.1126/SCIENCE.1234914

(-) Compounds

Molecule 1 - D25 ANTIGEN-BINDING FRAGMENT HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - D25 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - FUSION GLYCOPROTEIN F0
    Chains: F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Plasmid: PAH
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: F, FUSION GLYCOPROTEIN
    Mutation: YES
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS
    Organism Taxid: 11259
    Strain: A2
    Synonym: PROTEIN F, FUSION GLYCOPROTEIN F2, FUSION GLYCOPROTEIN F1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : FHL
Biological Unit 1 (3x): FHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4JHW)

(-) Sites  (0, 0)

(no "Site" information available for 4JHW)

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1F:37 -F:439
2F:69 -F:212
3F:313 -F:343
4F:322 -F:333
5F:358 -F:367
6F:382 -F:393
7F:416 -F:422
8H:22 -H:92
9H:140 -H:196
10L:23 -L:88
11L:134 -L:194

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly H:133 -Gly H:134
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Ser L:7 -Pro L:8
5Leu L:94 -Pro L:95
6Tyr L:140 -Pro L:141
7Lys F:65 -Glu F:66
8Thr F:245 -Pro F:246

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4JHW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4JHW)

(-) Exons   (0, 0)

(no "Exon" information available for 4JHW)

(-) 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:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeeeeeeeeee..eeeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhhhhhhhh...eeeeee...eeeeeeeeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..ee........hhhhhhhhhh....hhhhhhhhhhhhhhhhhh.eeee......eeeeeeeeee...eeeeeeeeee..ee..........eeee...eeeee....eeee.....eeee..eeee.....eeehhhhhhhhhh.........eeee.....eeee...eeeee......eeeee...eeeee....eeeee.....eeee..eeee.......eeee...hhhhhh............hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jhw F   26 QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAFIRKSDELL  513
                                    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         
                                                                                                  97|                                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                  137                                                                                                                                                                                                                                                                                                                                                                                        


Chain H from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee......eeeeeee....eeee.......eeeeee....eeeeee...hhhhheeeeeeeee..............ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jhw H    1 QVQLVQSGAEVKKPGSSVMVSCQASGGPLRNYIINWLRQAPGQGPEWMGGIIPVLGTVHYAPKFQGRVTITADESTDTAYIHLISLRSEDTAMYYCATETALVVSTTYLPHYFDNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|||    107       117       127       137       147       157       167       177       187       197       207      
                                                                              52A                            82A||               100A||||||||                                                                                                                 
                                                                                                              82B|                100B|||||||                                                                                                                 
                                                                                                               82C                 100C||||||                                                                                                                 
                                                                                                                                    100D|||||                                                                                                                 
                                                                                                                                     100E||||                                                                                                                 
                                                                                                                                      100F|||                                                                                                                 
                                                                                                                                       100G||                                                                                                                 
                                                                                                                                        100H|                                                                                                                 
                                                                                                                                         100I                                                                                                                 


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4jhw L    1 DIQMTQSPSSLSAAVGDRVTITCQASQDIVNYLNWYQQKPGKAPKLLIYVASNLETGVPSRFSGSGSGTDFSLTISSLQPEDVATYYCQQYDNLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 4JHW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4JHW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4JHW)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4jhw)
 
  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:133 - Gly H:134   [ RasMol ]  
    Leu L:94 - Pro L:95   [ RasMol ]  
    Lys F:65 - Glu F:66   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Thr F:245 - Pro F:246   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 
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  4jhw
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  FUS_HRSVA | P03420
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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 4mmq 4mmr 4mms 4mmt 4mmu 4mmv 4zyp 5c69 5c6b 5ea3 5ea4 5ea5 5ea6 5ea7 5ea8 5j3d 5k6b 5k6c 5k6f 5k6g 5k6h 5k6i 5toj 5tok 5tpn 5u68 5udc

(-) Related Entries Specified in the PDB File

4jha 'CRYSTAL STRUCTURE OF RSV-NEUTRALIZING HUMAN ANTIBODY D25'