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(-) Description

Title :  CRYSTAL STRUCTURE OF MOTAVIZUMAB FAB BOUND TO PEPTIDE EPITOPE
 
Authors :  J. S. Mclellan, M. Chen, A. Kim, Y. Yang, B. S. Graham, P. D. Kwong
Date :  04 Sep 09  (Deposition) - 19 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,H,L,P
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Fab, Rsv, Synagis, Motavizumab, Monoclonal, Complex, Cell Membrane, Cleavage On Pair Of Basic Residues, Disulfide Bond, Envelope Protein, Fusion Protein, Glycoprotein, Lipoprotein, Membrane, Palmitate, Transmembrane, Virion, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Mclellan, M. Chen, A. Kim, Y. Yang, B. S. Graham, P. D. Kwong
Structural Basis Of Respiratory Syncytial Virus Neutralization By Motavizumab.
Nat. Struct. Mol. Biol. V. 17 248 2010
PubMed-ID: 20098425  |  Reference-DOI: 10.1038/NSMB.1723

(-) Compounds

Molecule 1 - MOTAVIZUMAB FAB LIGHT CHAIN
    Chains: L, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293F CELLS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HUMANIZED-MOUSE ANTIBODY
 
Molecule 2 - MOTAVIZUMAB FAB HEAVY CHAIN
    Chains: H, A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: 293F CELLS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HUMANIZED-MOUSE ANTIBODY
 
Molecule 3 - FUSION GLYCOPROTEIN F1
    Chains: P, C
    Fragment: SEQUENCE DATABASE RESIDUES 254-277
    Organism Scientific: HUMAN RESPIRATORY SYNCYTIAL VIRUS
    Organism Taxid: 11259
    Strain: A2
    Synonym: FUSION GLYCOPROTEIN F0, PROTEIN F

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCHLP
Biological Unit 1 (1x):    HLP
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NH22Mod. Amino AcidAMINO GROUP
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2EDO2Ligand/Ion1,2-ETHANEDIOL
3NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:53 , ASP A:55 , ASP H:54 , SER P:259 , ASP P:263BINDING SITE FOR RESIDUE EDO P 1
2AC2SOFTWAREASN A:82B , MET A:82C , ASP A:83 , LEU H:170BINDING SITE FOR RESIDUE EDO A 219
3AC3SOFTWARESER C:259 , ASP C:263 , TRP H:53 , ASP H:55BINDING SITE FOR RESIDUE EDO C 2

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2A:140 -A:196
3B:23 -B:88
4B:134 -B:194
5H:22 -H:92
6H:140 -H:196
7L:23 -L:88
8L:134 -L:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Lys H:64 -Asp H:65
5Phe H:146 -Pro H:147
6Glu H:148 -Pro H:149
7Ser B:7 -Pro B:8
8Tyr B:94 -Pro B:95
9Tyr B:140 -Pro B:141
10Lys A:64 -Asp A:65
11Phe A:146 -Pro A:147
12Glu A:148 -Pro A:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IXT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IXT)

(-) Exons   (0, 0)

(no "Exon" information available for 3IXT)

(-) 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:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ixtA01 A:1-113 Immunoglobulins                                                                                         3ixtA02 A:114-212 Immunoglobulins                                                          - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee......eeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeeeeee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ixt A    1 QVTLRESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIRQPPGKALEWLADIWWDDKKHYNPSLKDRLTISKDTSKNQVVLKVTNMDPADTATYYCARDMIFNFYFDVWGQGTTVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||103       113       123  ||   141       151       161       171       181       191       201       211  
                                                             35A|                                             82A||               100A|                       126|                                                                              
                                                              35B                                              82B|                100B                        135                                                                              
                                                                                                                82C                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains d3ixtb1 B:1-107 automated matches                                                                         d3ixtb2 B:108-211 automated matches                                                                      SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------3ixtB02 B:109-211 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeeeeeee...eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3ixt B    1 DIQMTQSPSTLSASVGDRVTITCSASSRVGYMHWYQQKPGKAPKLLIYDTSKLASGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCFQGSGYPFTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR  211
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
                                                     27|                                                                                                                                                                                      
                                                      29                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:26
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:26
                                   262       272      
           FUS_HRSVA    253 TNSELLSLINDMPITNDQKKLMSNNV  278
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                3ixt C  253 xNSELLSLINDMPITNDQKKLMSNNx  278
                            |      262       272     |
                            |                      278-NH2
                          253-ACE                     


Chain H from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ixtH01 H:1-113 Immunoglobulins                                                                                         3ixtH02 H:114-212 Immunoglobulins                                                           - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee......eeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeee..eeeeeee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ixt H    1 QVTLRESGPALVKPTQTLTLTCTFSGFSLSTAGMSVGWIRQPPGKALEWLADIWWDDKKHYNPSLKDRLTISKDTSKNQVVLKVTNMDPADTATYYCARDMIFNFYFDVWGQGTTVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||103       113       123   ||  140       150       160       170       180       190       200       210   
                                                             35A|                                             82A||               100A|                        127|                                                                              
                                                              35B                                              82B|                100B                         135                                                                              
                                                                                                                82C                                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                    
               SCOP domains d3ixtl1 L:1-107 automated matches                                                                         d3ixtl2 L:108-212 automated matches                                                                       SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------3ixtL02 L:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeeeeeee...eeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3ixt L    1 DIQMTQSPSTLSASVGDRVTITCSASSRVGYMHWYQQKPGKAPKLLIYDTSKLASGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCFQGSGYPFTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
                                                     27|                                                                                                                                                                                       
                                                      29                                                                                                                                                                                       


Chain P from PDB  Type:PROTEIN  Length:26
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:26
                                   262       272      
           FUS_HRSVA    253 TNSELLSLINDMPITNDQKKLMSNNV  278
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                3ixt P  253 xNSELLSLINDMPITNDQKKLMSNNx  278
                            |      262       272     |
                            |                      278-NH2
                          253-ACE
   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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Mouse (Mus musculus) (152)
1a3ixtL02L:109-212
1b3ixtB02B:109-211
1c3ixtH02H:114-212
1d3ixtA02A:114-212
1e3ixtA01A:1-113
1f3ixtH01H:1-113

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IXT)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain C,P   (FUS_HRSVA | P03420)
biological process
    GO:0019064    fusion of virus membrane with host plasma membrane    Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
    GO:0006948    induction by virus of host cell-cell fusion    The process of syncytia-forming cell-cell fusion, caused by a virus.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0060141    positive regulation of syncytium formation by virus    The process in which a virus increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        FUS_HRSVA | P03420: 2mdp 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 5tok 5tpn 5u68 5udc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3IXT)