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(-) Description

Title :  CRYSTAL STRUCTURE OF HBR3 BOUND TO CB3S-FAB
 
Authors :  S. G. Hymowitz
Date :  23 Jun 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  H,L,R
Keywords :  Fab Fragment, Tnfrsf, Antibody-Receptor Complex, Crd, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. V. Lee, S. G. Hymowitz, H. J. Wallweber, N. C. Gordon, K. L. Billeci, S. P. Tsai, D. M. Compaan, J. Yin, Q. Gong, R. F. Kelley, L. E. Deforge, F. Martin, M. A. Starovasnik, G. Fuh
Synthetic Anti-Br3 Antibodies That Mimic Baff Binding And Target Both Human And Murine B Cells.
Blood V. 108 3103 2006
PubMed-ID: 16840730  |  Reference-DOI: 10.1182/BLOOD-2006-03-011031

(-) Compounds

Molecule 1 - CB3S FAB LIGHT CHAIN (KAPPA)
    Chains: L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: 4B8
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PROTEIN SELECTED BY PHAGE DISPLAY
 
Molecule 2 - CB3S FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: 4B8
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: PROTEIN SELECTED BY PHAGE DISPLAY
 
Molecule 3 - TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 13C
    Chains: R
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-32A
    Expression System Strain: ORIGAMI (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CYSTEINE RICH DOMAIN (RESIDUES 7-54)
    Gene: TNFRSF13C, BAFFR, BR3
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: B CELL-ACTIVATING FACTOR RECEPTOR, BAFF RECEPTOR, BAFF-R, BLYS RECEPTOR 3, CD268 ANTIGEN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLR

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2HFG)

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:97 -H:100D
3H:140 -H:196
4L:23 -L:88
5L:133 -L:193
6R:19 -R:32
7R:24 -R:35

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Ser L:94 -Pro L:95
3Tyr L:139 -Pro L:140
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002912321ENSE00001175504chr22:42322822-42322642181TR13C_HUMAN1-46461R:13-3927
1.2ENST000002912322ENSE00001048605chr22:42322335-42322105231TR13C_HUMAN46-123780--
1.3ENST000002912323ENSE00001201908chr22:42321558-42321045514TR13C_HUMAN123-184620--

(-) 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:220
 aligned with Q6N093_HUMAN | Q6N093 from UniProtKB/TrEMBL  Length:417

    Alignment length:226
                                                        1                                                                   70   71    77 78                                                                                                                  
                                     -         -        |2        12        22        32        42        52        62       | -  |     |- |      86        96       106       116       126       136       146       156       166       176       186      
        Q6N093_HUMAN      - ----------------------------FFNYAMHWVRQAPGKGLEWVAVIAYDGSTQYYADSVRGRFTVSRDNSANTLFLEMNSLRPEDTAVYYCAK----AHSGTSK--FDPWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERK  192
               SCOP domains d2hfgh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                               d2hfgh2 H:114-      214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                 SCOP domains
               CATH domains 2hfgH01 H:1-113 Immunoglobulins                                                                                              2hfgH02 H:114-      214 Immunoglobulins                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeee..eeeeeeeee...eeeee........eeeee...------.eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2hfg H    1 EVQLVESGGGLVQPGGSLRLSCAASGFTISSSSIHWVRQAPGKGLEWVAWVLPSVGFTDYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARRVCYNRLGVCAGGMDYWGQGTLVTVSSASTKGPSVFPLAPS------GTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  214
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||     108       118        |-     | 138       148       158       168       178       188       198       208      
                                                                              52A                            82A||               100A|||||||                        127    134                                                                                
                                                                                                              82B|                100B||||||                                                                                                                  
                                                                                                               82C                 100C|||||                                                                                                                  
                                                                                                                                    100D||||                                                                                                                  
                                                                                                                                     100E|||                                                                                                                  
                                                                                                                                      100F||                                                                                                                  
                                                                                                                                       100G|                                                                                                                  
                                                                                                                                        100H                                                                                                                  


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d2hfgl1 L:1-106A automated matches                                                                         d2hfgl2 L:107-212 automated matches                                                                        SCOP domains
               CATH domains 2hfgL01 L:1-107 Immunoglobulins                                                                             2hfgL02 L:108-212 Immunoglobulins                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2hfg L    1 DIQMTQSPSSLSASVGDRVTITCRASQDVSTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSQISPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  212
                                    10        20        30        40        50        60        70        80        90       100      |109       119       129       139       149       159       169       179       189       199       209   
                                                                                                                                   106A                                                                                                          


Chain R from PDB  Type:PROTEIN  Length:27
 aligned with TR13C_HUMAN | Q96RJ3 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:27
                                    22        32       
         TR13C_HUMAN     13 APAPTPCVPAECFDLLVRHCVACGLLR   39
               SCOP domains d2hfgr_ R:                  SCOP domains
               CATH domains --------------------------- CATH domains
               Pfam domains --------------------------- Pfam domains
         Sec.struct. author ..........eeee....eeee.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------- SAPs(SNPs)
                    PROSITE --------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: R:13-39      Transcript 1
                2hfg R   13 APAPTPCNPAECFDPLVRHCVACGLLR   39
                                    22        32
   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  (5, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (Q6N093_HUMAN | Q6N093)

Chain R   (TR13C_HUMAN | Q96RJ3)
biological process
    GO:0031296    B cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B cell receptor to augment B cell activation.
    GO:0001782    B cell homeostasis    The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0030890    positive regulation of B cell proliferation    Any process that activates or increases the rate or extent of B cell proliferation.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0002636    positive regulation of germinal center formation    Any process that activates or increases the frequency, rate, or extent of germinal center formation.
    GO:0045078    positive regulation of interferon-gamma biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    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: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: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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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        TR13C_HUMAN | Q96RJ3: 1mpv 1oqe 1osx 3v56 4v46

(-) Related Entries Specified in the PDB File

2hff