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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AN NNA7 FAB THAT RECOGNIZES AN N-TYPE BLOOD GROUP ANTIGEN
 
Authors :  K. Xie, S. C. Song, S. L. Spitalnik, J. E. Wedekind
Date :  22 Apr 04  (Deposition) - 07 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fab, Glycophorin A, Blood Group Antigen, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Xie, S. C. Song, S. L. Spitalnik, J. E. Wedekind
Crystal Structure And Mutational Analysis Of An Antibody That Recognizes An N-Type Blood Group Antigen
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB NNA7 HEAVY CHAIN
    ChainsL
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOMB3H
    Expression System StrainSURE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneN92 IGG2A
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsMONOCLONAL ANTIBODY
 
Molecule 2 - FAB NNA7 LIGHT CHAIN
    ChainsH
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCOMB3H
    Expression System StrainSURE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneN92 L CHAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsPHAGE DISPLAY MODIFIED

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY H:34 , TRP H:53 , SER H:54 , ASN H:99 , TYR H:104 , PRO H:206 , THR H:210 , LYS H:211BINDING SITE FOR RESIDUE MES H 801
2AC2SOFTWARELYS L:113 , ARG L:161 , ARG L:194 , HIS L:195 , HOH L:818 , HOH L:839 , HOH L:847BINDING SITE FOR RESIDUE GOL L 701
3AC3SOFTWARETYR H:104 , PRO H:206 , SER H:209 , HOH H:820 , HOH H:844 , HOH H:911 , HIS L:32 , GLY L:97BINDING SITE FOR RESIDUE GOL H 702

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:23 -H:96
2H:146 -H:201
3L:24 -L:94
4L:140 -L:200

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:8 -Pro L:9
2Val L:100 -Pro L:101
3Tyr L:146 -Pro L:147
4Phe H:152 -Pro H:153
5Glu H:154 -Pro H:155
6Trp H:194 -Pro H:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T2Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T2Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1T2Q)

(-) 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:217
 aligned with HVM45_MOUSE | P01821 from UniProtKB/Swiss-Prot  Length:116

    Alignment length:217
                                  26                                                                                                                                                                                                                 
                                25 |                                                                                       116                                                                                                                       
                                 | |28        38        48        58        68        78        88        98       108       | -         -         -         -         -         -         -         -         -         -         -         -       
          HVM45_MOUSE    20 QVQLKQ-SGPGLVQPSQSLSITCTVSGFSLTSYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSQVFFKMNSLQSNDTAIYYCAR-----------------------------------------------------------------------------------------------------------------------   -
               SCOP domains -----------------------------------------------------------------------------------------------------------------------d1t2qh1 H:120-220 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                  - SCOP domains
               CATH domains 1t2qH01 H:1-119 Immunoglobulins                                                                                        1t2qH02 H:120-218 Immunoglobulins                                                              --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...ee.....eeeeeeee........eeeeeee...eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee.hhhh.eeee...eeeee........eeeee......eeeeeeeeeee.....eeee.hhh....eee........eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t2q H   1 EVQLLEESGPGLVQPSQSLSITCTVSGFSLTSYGVHWVRQSPGKGLEWLGVIWSGGSTDYNAAFISRLSISKDNSKSQVFFKMNSLQADDTAIYYCARNRGYSYAMDSWGQGTSVTVSSAKTTPPSVYPLAPGSASMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    || 144       154       164       174       184       194       204       214       
                                                                                                                                                                135|                                                                                 
                                                                                                                                                                 140                                                                                 

Chain L from PDB  Type:PROTEIN  Length:217
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 217
               SCOP domains d1t2ql1 L:2-114 automated matches                                                                                d1t2ql2 L:115-218 automated matches                                                                      SCOP domains
               CATH domains 1t2qL01 L:2-114 Immunoglobulins                                                                                  -1t2qL02 L:116-215 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t2q L   2 ELVMTQSPLSLPVSLGDQASISCRSSQSLVHSSGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLTISRVEAEDLGVYYCFQGSHVPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1T2Q)

(-) Gene Ontology  (22, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM45_MOUSE | P01821)
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.

Chain L   (A2NHM3_MOUSE | A2NHM3)

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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM34p3d
        IGHG1_MOUSE | P018681ahw 1ai1 1bm3 1clo 1ct8 1dba 1dbb 1dbj 1dbk 1dbm 1emt 1fbi 1fdl 1fns 1gpo 1k4d 1kel 1kem 1mf2 1mlc 1n5y 1n6q 1ntl 1oak 1opg 1p2c 1p7k 1r0a 1r3i 1r3j 1r3k 1r3l 1rih 1seq 1yed 2aty 2b2x 2dbl 3zo0
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM31cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1zea 2a1w 2dqt 2dqu 2dtm 2ipt 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1T2Q)