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(-) Description

Title :  EPITOPE CHARACTERIZATION AND CRYSTAL STRUCTURE OF GA101 PROVIDE INSIGHTS INTO THE MOLECULAR BASIS FOR THE TYPE I / TYPE II DISTINCTION OF ANTI- CD20 ANTIBODIES
 
Authors :  K. -P. Hopfner, A. Lammens
Date :  24 Nov 10  (Deposition) - 13 Apr 11  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  H,I,K,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,K  (1x)
Keywords :  Antibody Fab-Fragment Ig-Domain, Antibody, Cd20, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Niederfellner, A. Lammens, O. Mundigl, G. J. Georges, W. Schaefer, M. Schwaiger, A. Franke, K. Wiechmann, S. Jenewein, J. W. Slootstra, P. Timmerman, A. Brannstrom, F. Lindstrom, E. Mossner, P. Umana, K. P. Hopfner, C. Klein
Epitope Characterization And Crystal Structure Of Ga101 Provide Insights Into The Molecular Basis For Type I/Ii Distinction Of Cd20 Antibodies.
Blood V. 118 358 2011
PubMed-ID: 21444918  |  Reference-DOI: 10.1182/BLOOD-2010-09-305847

(-) Compounds

Molecule 1 - GA101 FAB HEAVY CHAIN
    Chains: H, I
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHINESE HAMSTER OVARY (CHO)
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - GA101 FAB LIGHT CHAIN
    Chains: L, K
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHINESE HAMSTER OVARY (CHO)
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HIKL
Biological Unit 1 (1x): H  L
Biological Unit 2 (1x):  IK 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3PP3)

(-) Sites  (0, 0)

(no "Site" information available for 3PP3)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:146 -H:202
3I:22 -I:96
4I:146 -I:202
5K:23 -K:93
6K:139 -K:199
7L:23 -L:93
8L:139 -L:199

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Phe H:152 -Pro H:153
2Glu H:154 -Pro H:155
3Thr L:7 -Pro L:8
4Leu L:99 -Pro L:100
5Tyr L:145 -Pro L:146
6Phe I:152 -Pro I:153
7Glu I:154 -Pro I:155
8Thr K:7 -Pro K:8
9Leu K:99 -Pro K:100
10Tyr K:145 -Pro K:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PP3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PP3)

(-) Exons   (0, 0)

(no "Exon" information available for 3PP3)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee...eeeeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeehhhhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pp3 H   1 QVQLVQSGAEVKKPGSSVKVSCKASGYAFSYSWINWVRQAPGQGLEWMGRIFPGDGDTDYNGKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARNVFDGYWLVYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain I from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee.........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pp3 I   1 QVQLVQSGAEVKKPGSSVKVSCKASGYAFSYSWINWVRQAPGQGLEWMGRIFPGDGDTDYNGKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARNVFDGYWLVYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain K from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3pp3k1 K:1-112 automated matches                                                                               d3pp3k2 K:113-219 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pp3 K   1 DIVMTQTPLSLPVTPGEPASISCRSSKSLLHSNGITYLYWYLQKPGQSPQLLIYQMSNLVSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCAQNLELPYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3pp3l1 L:1-112 automated matches                                                                               d3pp3l2 L:113-219 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee......eeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pp3 L   1 DIVMTQTPLSLPVTPGEPASISCRSSKSLLHSNGITYLYWYLQKPGQSPQLLIYQMSNLVSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCAQNLELPYTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PP3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PP3)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3PP3)

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  Cis Peptide Bonds
    Glu H:154 - Pro H:155   [ RasMol ]  
    Glu I:154 - Pro I:155   [ RasMol ]  
    Leu K:99 - Pro K:100   [ RasMol ]  
    Leu L:99 - Pro L:100   [ RasMol ]  
    Phe H:152 - Pro H:153   [ RasMol ]  
    Phe I:152 - Pro I:153   [ RasMol ]  
    Thr K:7 - Pro K:8   [ RasMol ]  
    Thr L:7 - Pro L:8   [ RasMol ]  
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    Tyr L:145 - Pro L:146   [ RasMol ]  
 
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3pp4 GA101 FAB BOUND TO CD20 PEPTIDE