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(-) Description

Title :  CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI-TGFALPHA ANTIBODY FAB-FRAGMENT
 
Authors :  M. Hahn, D. Winkler, R. Misselwitz, H. Wessner, K. Welfle, G. Zahn, J. Schneider-Mergener, W. Hoehne
Date :  12 Jul 00  (Deposition) - 12 Jul 01  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  H,I,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
Keywords :  Immune System, Complex (Antibody/Antigen), Cross-Reactivity, Protein-Peptide Recognition (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Hahn, D. Winkler, K. Welfle, R. Misselwitz, H. Welfle, H. Wessner, G. Zahn, C. Scholz, M. Seifert, R. Harkins, J. Schneider-Mergener, W. Hoehne
Cross-Reactive Binding Of Cyclic Peptides To An Anti-Tgf Alpha Antibody Fab Fragment: An X-Ray Structural And Thermodynamic Analysis
J. Mol. Biol. V. 314 293 2001
PubMed-ID: 11718562  |  Reference-DOI: 10.1006/JMBI.2001.5135

(-) Compounds

Molecule 1 - TAB2
    Cell LineMOUSE HYBRIDOMA
    ChainsL, M
    FragmentIG KAPPA LIGHT CHAIN
    OrganSPLEEN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsMURINE FAB-FRAGMENT
    StrainBALB/C
 
Molecule 2 - TAB2
    Cell LineMOUSE HYBRIDOMA
    ChainsH
    FragmentIG KAPPA HEAVY CHAIN
    OrganSPLEEN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsMURINE FAB-FRAGMENT
 
Molecule 3 - TAB2
    Cell LineMOUSE HYBRIDOMA
    ChainsI
    FragmentIG KAPPA HEAVY CHAIN
    OrganSPLEEN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsMURINE FAB-FRAGMENT
 
Molecule 4 - CYCLIC PEPTIDE
    ChainsP, Q
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit HILMPQ
Biological Unit 1 (1x)H L P 
Biological Unit 2 (1x) I M Q

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1E4X)

(-) Sites  (0, 0)

(no "Site" information available for 1E4X)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:125 -L:214
3H:137 -H:192
4I:22 -I:92
5I:125 -M:214
6I:137 -I:192
7L:23 -L:88
8L:134 -L:194
9M:23 -M:88
10M:134 -M:194

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Phe H:143 -Pro H:144
2Glu H:145 -Pro H:146
3Trp H:185 -Pro H:186
4Phe I:143 -Pro I:144
5Glu I:145 -Pro I:146
6Trp I:185 -Pro I:186
7Thr L:7 -Pro L:8
8Leu L:94 -Pro L:95
9Tyr L:140 -Pro L:141
10Thr M:7 -Pro M:8
11Leu M:94 -Pro M:95
12Tyr M:140 -Pro M:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E4X)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_MOUSE84-90
 
  2L:192-198
M:192-198
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_MOUSE84-90
 
  1L:192-198
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGKC_MOUSE84-90
 
  1-
M:192-198

(-) Exons   (0, 0)

(no "Exon" information available for 1E4X)

(-) 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 H from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1e4xh1 H:1-110 Immunoglobulin heavy chain variable domain, VH                                                    d1e4xh2 H:111-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1e4xH01 H:1-110 Immunoglobulins                                                                                   1e4xH02 H:111-209 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeee.......eeeeeee.....eeeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e4x H   1 QVQLQQPGAELVKPGASVKLSCKASGFTFTNYWMHWVKQRPGQGLEWIGEILPSNGRTNYNEKFKTKATLTVDKSSNTAYMQLSSLTSEDSAVYYCARSPSDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRVP 212
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                                              52A                            82A||                                                                                                                                  
                                                                                                              82B|                                                                                                                                  
                                                                                                               82C                                                                                                                                  

Chain I from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1e4xi1 I:1-110 Immunoglobulin heavy chain variable domain, VH                                                    d1e4xi2 I:111-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1e4xI01 I:1-110 Immunoglobulins                                                                                   1e4xI02 I:111-209 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4x I   1 QVQLQQPGAELVKPGPSVKLSCKASGFTFTNYWMHWVKQRPGQGLEWIGEILPSNGRTNYNEKFKTKATLTVDKSSNTAYMQLSSLTSEDSAVYYCARSPSDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRVPI 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                                              52A                            82A||                                                                                                                                   
                                                                                                              82B|                                                                                                                                   
                                                                                                               82C                                                                                                                                   

Chain L from PDB  Type:PROTEIN  Length:214
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:214
                                                                                                                                        1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102    
           IGKC_MOUSE     - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 106
               SCOP domains d1e4xl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1e4xl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1e4xL01 L:1-108 Immunoglobulins                                                                             1e4xL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4x L   1 DIQMTQTPSSLSASLGDRVTISCRASQDISHYLNWFQQKPDGTVKLLIYYTSTLHSGVPSRFSGSGSGTDYSLTISNLEEEDIAFYFCQQGGALPFTFGSGTKLAIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLDSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    

Chain M from PDB  Type:PROTEIN  Length:214
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:214
                                                                                                                                        1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102    
           IGKC_MOUSE     - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 106
               SCOP domains d1e4xm1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1e4xm2 M:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1e4xM01 M:1-107 Immunoglobulins                                                                            1e4xM02 M:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeee.......eeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4x M   1 DIQMTQTPSSLSASLGDRVTISCRASQDISHYLNWFQQKPDGTVKLLIYYTSTLHSGVPSRFSGSGSGTDYSLTISNLEEEDIAFYFCQQGGALPFTFGSGTKLAIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLDSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    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:7
                                       
               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
                 1e4x P   1 VVSHFND   7

Chain Q from PDB  Type:PROTEIN  Length:7
                                       
               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
                 1e4x Q   1 VVSHFND   7

   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  (4, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a1e4xM02M:108-211
1b1e4xH02H:111-209
1c1e4xI02I:111-209
1d1e4xL02L:109-211
1e1e4xH01H:1-110
1f1e4xI01I:1-110
1g1e4xM01M:1-107
1h1e4xL01L:1-108

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E4X)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain L,M   (IGKC_MOUSE | P01837)
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:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    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.

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    Glu H:145 - Pro H:146   [ RasMol ]  
    Glu I:145 - Pro I:146   [ RasMol ]  
    Leu L:94 - Pro L:95   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGKC_MOUSE | P0183715c8 1a0q 1a3l 1ahw 1ai1 1aif 1c12 1cf8 1cfn 1cfq 1cfs 1cft 1cic 1ck0 1ct8 1dqj 1dqm 1dqq 1e4w 1ehl 1emt 1f11 1fai 1fbi 1fdl 1fe8 1fgn 1fj1 1fl3 1fns 1frg 1fsk 1gpo 1hh6 1hh9 1hi6 1i8m 1iai 1igy 1jnl 1jnn 1jrh 1k4c 1k4d 1kb5 1kc5 1kcr 1kcs 1kcu 1kcv 1ken 1kno 1lo0 1mf2 1mh5 1mlb 1mlc 1n5y 1n6q 1nby 1nbz 1ndg 1ndm 1oak 1ob1 1orq 1ors 1osp 1ots 1ott 1otu 1p2c 1p7k 1psk 1q9o 1q9w 1qgc 1r0a 1r24 1r3i 1r3j 1r3k 1r3l 1rih 1ruq 1rur 1s5h 1seq 1t03 1t4k 1ub5 1ub6 1uwx 1xf2 1xf3 1xf4 1xgp 1xgq 1xgu 25c8 2a6d 2a6k 2adf 2adj 2ajs 2aju 2ajv 2ajx 2ajy 2ajz 2ak1 2bob 2boc 2ck0 2f19 2fr4 2g5b 2h8p 2hg5 2hrp 2mpa 2nr6 2q76 2r1w 2r1y 2r23 2r2b 2uyl 2v17 2v7h 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr 2vl5 2vq1 2vwe 2w60 2w65 2w9d 2w9e 2z91 2z92 2z93 2zjs 35c8 3bae 3bgf 3bkc 3bkj 3bkm 3bpc 3bqu 3bsz 3bt2 3bz4 3c5s 3c6s 3cfb 3cfc 3cfd 3cfe 3ck0 3cle 3clf 3cmo 3cvh 3cvi 3d9a 3ejz 3eot 3f7v 3f7y 3fb6 3hfm 4kk5 4kk8 4qnp 4zxb 6fab

(-) Related Entries Specified in the PDB File

1e4w CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI-TGFALPHA ANTIBODY FAB-FRAGMENT
1fbi FAB FRAGMENT OF THE MONOCLONAL ANTIBODY F9.13.7 (IGG1) COMPLEXED WITH LYSOZYME