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(-) Description

Title :  STRUCTURE OF AN EBOLAVIRUS-PROTECTIVE ANTIBODY IN COMPLEX WITH ITS MUCIN-DOMAIN LINEAR EPITOPE
 
Authors :  D. O. Olal, A. Kuehne, J. E. Lee, S. Bale, J. M. Dye, E. O. Saphire
Date :  25 Jan 11  (Deposition) - 11 Jan 12  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  C,D,H,L,P,Q
Biol. Unit 1:  C,D,P  (1x)
Biol. Unit 2:  H,L,Q  (1x)
Keywords :  Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. O. Olal, A. Kuehne, S. Bale, P. Halfmann, T. Hashiguchi, M. L. Fusco, J. E. Lee, L. B. King, Y. Kawaoka, J. M. Dye, E. O. Saphire
Structure Of An Ebola Virus-Protective Antibody In Complex With Its Mucin-Domain Linear Epitope.
J. Virol. V. 86 2809 2012
PubMed-ID: 22171276  |  Reference-DOI: 10.1128/JVI.05549-11

(-) Compounds

Molecule 1 - LIGHT CHAIN
    Chains: C, L
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Strain: BALB/C
 
Molecule 2 - HEAVY CHAIN
    Chains: D, H
    Organ: SPLEEN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
    Strain: BALB/C
 
Molecule 3 - ENVELOPE GLYCOPROTEIN
    Chains: P, Q
    Fragment: RESIDUES 477-493
    Organism Scientific: ZAIRE EBOLAVIRUS
    Organism Taxid: 128951
    Strain: ZAIRE-95
    Synonym: GP, GP1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : CDHLPQ
Biological Unit 1 (1x): CD  P 
Biological Unit 2 (1x):   HL Q

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2Y6S)

(-) Sites  (0, 0)

(no "Site" information available for 2Y6S)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1C:23 -C:92
2C:138 -C:198
3D:22 -D:96
4D:140 -D:195
5H:22 -H:96
6H:140 -H:195
7L:23 -L:92
8L:138 -L:198

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Ser C:7 -Pro C:8
2Ala C:80 -Pro C:81
3Leu C:98 -Thr C:99
4Tyr C:144 -Pro C:145
5Phe D:146 -Pro D:147
6Glu D:148 -Pro D:149
7Trp D:188 -Pro D:189
8Phe H:146 -Pro H:147
9Glu H:148 -Pro H:149
10Trp H:188 -Pro H:189
11Ser L:7 -Pro L:8
12Ala L:80 -Pro L:81
13Leu L:98 -Thr L:99
14Tyr L:144 -Pro L:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y6S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y6S)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y6S)

(-) 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 C from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee.....eeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6s C   1 DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYSYMHWNQQKPGQPPRLLIYLVSNLESGVPARFSGSGSGTDFTLNIAPVEEEDAATYYCQHIAELTRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain D from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh...eeeeehhh.eeeeee...hhhhheeeeeee........eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6s D   1 QVQLQQSGPELVKPGASVKMSCKASGYTFTDYVISWVKQRTGQGLEWIGEFYPGTDSTYYTENFKGRATLTADKSSKTAYMQLSSLTSEDSAVYFCATAFDYWGQGTTLTVSSAATTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 213
                                    10        20        30        40        50        60        70        80        90       100       110       120     ||137       147       157       167       177       187       197       207      
                                                                                                                                                       126|                                                                               
                                                                                                                                                        134                                                                               


Chain H from PDB  Type:PROTEIN  Length:206
                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh...eeeeehhh.eeeeee...hhhhheeeeeee........eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6s H   1 QVQLQQSGPELVKPGASVKMSCKASGYTFTDYVISWVKQRTGQGLEWIGEFYPGTDSTYYTENFKGRATLTADKSSKTAYMQLSSLTSEDSAVYFCATAFDYWGQGTTLTVSSAATTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 213
                                    10        20        30        40        50        60        70        80        90       100       110       120     ||137       147       157       167       177       187       197       207      
                                                                                                                                                       126|                                                                               
                                                                                                                                                        134                                                                               


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee.....eeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6s L   1 DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYSYMHWNQQKPGQPPRLLIYLVSNLESGVPARFSGSGSGTDFTLNIAPVEEEDAATYYCQHIAELTRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain P from PDB  Type:PROTEIN  Length:15
 aligned with VGP_EBOZ5 | P87666 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:15
                                   487     
            VGP_EBOZ5   478 KLGLITNTIAGVAGL 492
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 2y6s P 478 KLGLITNTIAGVAGL 492
                                   487     


Chain Q from PDB  Type:PROTEIN  Length:15
 aligned with VGP_EBOZ5 | P87666 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:15
                                   487     
            VGP_EBOZ5   478 KLGLITNTIAGVAGL 492
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 2y6s Q 478 KLGLITNTIAGVAGL 492
                                   487
   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 2Y6S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y6S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y6S)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain P,Q   (VGP_EBOZ5 | P87666)
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    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:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    GO:0039587    suppression by virus of host tetherin activity    Any process in which a virus stops, prevents, or reduces the activity of host tetherin activity. Tetherin (also known as BST2) is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses. By blocking tetherin activity, many viruses circumvent its antiviral effects.
    GO:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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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  Cis Peptide Bonds
    Ala C:80 - Pro C:81   [ RasMol ]  
    Ala L:80 - Pro L:81   [ RasMol ]  
    Glu D:148 - Pro D:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Leu C:98 - Thr C:99   [ RasMol ]  
    Leu L:98 - Thr L:99   [ RasMol ]  
    Phe D:146 - Pro D:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
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    Trp D:188 - Pro D:189   [ RasMol ]  
    Trp H:188 - Pro H:189   [ RasMol ]  
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    Tyr L:144 - Pro L:145   [ RasMol ]  
 
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  2y6s
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  VGP_EBOZ5 | P87666
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 Related Entries

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

UniProtKB/Swiss-Prot
        VGP_EBOZ5 | P87666: 3csy 5f1b 5hj3 5jnx

(-) Related Entries Specified in the PDB File

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