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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 13F6-1-2 FAB FRAGMENT BOUND TO ITS EBOLA VIRUS GLYCOPROTEIN PEPTIDE EPITOPE.
 
Authors :  J. E. Lee, A. Kuehne, D. M. Abelson, M. L. Fusco, M. K. Hart, E. O. Saphire
Date :  02 Jul 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  Immunologlobulin Fold, Antibody-Peptide Complex, Immune System/Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Lee, A. Kuehne, D. M. Abelson, M. L. Fusco, M. K. Hart, E. O. Saphire
Complex Of A Protective Antibody With Its Ebola Virus Gp Peptide Epitope: Unusual Features Of A V Lambda X Light Chain.
J. Mol. Biol. V. 375 202 2008
PubMed-ID: 18005986  |  Reference-DOI: 10.1016/J.JMB.2007.10.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 13F6-1-2 FAB FRAGMENT HEAVY CHAIN
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
 
Molecule 2 - 13F6-1-2 FAB FRAGMENT V LAMBDA X LIGHT CHAIN
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: HYBRIDOMA
 
Molecule 3 - ENVELOPE GLYCOPROTEIN PEPTIDE
    Chains: P
    Engineered: YES
    Fragment: ENVELOPE GLYCOPROTEIN PEPTIDE, RESIDUES 404-414
    Other Details: THE SEQUENCE OF THE PEPTIDE OCCURS IN EBOLAVIRUS (ZAIRE SUBTYPE) ENVELOPE GLYCOPROTEIN AS RESIDUES 404-414.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2QHR)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:140 -H:195
3L:23 -L:88
4L:135 -L:193

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Trp H:188 -Pro H:189
4Ser L:141 -Pro L:142

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.LAC2_MOUSE83-89  1L:191-197

(-) Exons   (0, 0)

(no "Exon" information available for 2QHR)

(-) 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 H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------d2qhrh1 H:115-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 2qhrH01 H:1-113 Immunoglobulins                                                                                            2qhrH02 H:114-212 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeeee..........eeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhhhhh..eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2qhr H    1 EVQVVESGGGLVKPGGSLKLSCAASGFAFSSYDMSWVRQTPEKRLEWVAYISRGGGYTYYPDTVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCSRHIYYGSSHYYAMDYWGQGTSVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  212
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       130       140       150       160       170       180       190       200       210  
                                                                              52A                            82A||               100A|||||                                                                                                                
                                                                                                              82B|                100B||||                                                                                                                
                                                                                                               82C                 100C|||                                                                                                                
                                                                                                                                    100D||                                                                                                                
                                                                                                                                     100E|                                                                                                                
                                                                                                                                      100F                                                                                                                


Chain L from PDB  Type:PROTEIN  Length:218
 aligned with LAC2_MOUSE | P01844 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:218
                                                                                                                                                1                                                                                                     
                                     -         -         -         -         -         -         -         -         -         -         -      |  4        14        24        34        44        54        64        74        84        94        
          LAC2_MOUSE      - --------------------------------------------------------------------------------------------------------------------QPKSTPTLTVFPPSSEELKENKATLVCLISNFSPSGVTVAWKANGTPITQGVDTSNPTKEGNKFMASSFLHLTSDQWRSHNSFTCQVTHEGDTVEKSLSPAE  102
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qhrL01 L:2-108 Immunoglobulins                                                                                     2qhrL02 L:109-208 Immunoglobulins                                                                   -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------C1-set-2qhrL01 L:120-205                                                              ----- Pfam domains
         Sec.struct. author ...ee...eeeee....eeeeeee.hhhh...eeeeee......eeeeee.....eee.......eeeeee..eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eee...eee..eeeeeeeeeeehhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qhr L    2 QLVLTQSSSASFSLGASAKLTCTLSRQHSTYTIEWYQQQPLKPPRYVMELKKDGSHSTGDGIPDRFSGSSSGADRYLSISNIQPEDEAIYICGVGDTIKEQFVYVFGGGTKVTVLGQPKSTPTLTVFPPSSEELKENKATLVCLISNFSPSGVTVAWKANGTPITQGVDTSNPTKEGNKFMASSFLHLTSDQWRSHNSFTCQVTHEGDTVEKSLSPAE  210
                                    11        21      | 30        40        50    ||||56        66        76        86       95A|||    102       112       122       132       142       152       162       172       182       192       202        
                                                    27A                         54A|||                                       95A|||                                                                                                                   
                                                                                 54B||                                        95B||                                                                                                                   
                                                                                  54C|                                         95C|                                                                                                                   
                                                                                   54D                                          95D                                                                                                                   


Chain P from PDB  Type:PROTEIN  Length:11
 aligned with VGP_EBOEC | P87671 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:11
                                   413 
           VGP_EBOEC    404 VEQHHRRTDND  414
               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
                2qhr P  404 VEQHHRRTDND  414
                                   413
   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  (1, 1)

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

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (LAC2_MOUSE | P01844)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0034987    immunoglobulin receptor binding    Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
    GO:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:0050871    positive regulation of B cell activation    Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0042571    immunoglobulin complex, circulating    An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain P   (VGP_EBOEC | P87671)
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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