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Asym./Biol. Unit (Jmol Viewer)

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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 :   1.60

Chains :   Asym./Biol. Unit : H,L,P

Keywords :   Antibody Fab Fragment Ig-Domain, Cd20, Cyclic Peptide, Antibody Antigen, 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

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

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

Molecule 3 - B-LYMPHOCYTE ANTIGEN CD20
	Chains	:	P
	Engineered	:	YES
	Fragment	:	LARGE EXTRACELLULAR LOOP (UNP RESIDUES 163-187)
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CD20
	Synonym	:	B-LYMPHOCYTE SURFACE ANTIGEN B1, BP35, LEUKOCYTE SURFACE ANTIGEN LEU-16, MEMBRANE-SPANNING 4-DOMAINS SUBFAMILY A MEMBER 1
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	H	L	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN H:35 , ARG H:50 , ASN H:99 , TYR L:101	BINDING SITE FOR RESIDUE CL H 225

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:96
2	H:146	-	H:202
3	L:23	-	L:93
4	L:139	-	L:199
5	P:167	-	P:183

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 3PP4)

(no "PROSITE Motif" information available for 3PP4)

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4a	ENST00000389939	4a	ENSE00001507321	chr11:60229654-60230006	353	CD20_HUMAN	1-53	53	0	-	-
1.5	ENST00000389939	5	ENSE00001107914	chr11:60230475-60230594	120	CD20_HUMAN	54-93	40	0	-	-
1.6c	ENST00000389939	6c	ENSE00001507320	chr11:60231761-60231817	57	CD20_HUMAN	94-112	19	0	-	-
1.7c	ENST00000389939	7c	ENSE00001107910	chr11:60233394-60233630	237	CD20_HUMAN	113-191	79	1	P:164-187	24
1.8b	ENST00000389939	8b	ENSE00001028073	chr11:60234432-60234533	102	CD20_HUMAN	192-225	34	0	-	-
1.9e	ENST00000389939	9e	ENSE00001107918	chr11:60235723-60238225	2503	CD20_HUMAN	226-297	72	0	-	-

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
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee....eeeee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pp4 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 L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pp4 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

Chain P from PDB  Type:PROTEIN  Length:24
 aligned with CD20_HUMAN | P11836 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:24
                                   173       183    
           CD20_HUMAN   164 IYNCEPANPSEKNSPSTQYCYSIQ 187
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains CD20-3pp4P01 P:164-187   Pfam domains
         Sec.struct. author .......hhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
               Transcript 1 Exon 1.7c  PDB: P:164-18 Transcript 1
                 3pp4 P 164 IYNCEPANPSEKNSPSTQYCYSIQ 187
                                   173       183

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 '\|'

(no "SCOP Domain" information available for 3PP4)

(no "CATH Domain" information available for 3PP4)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Tetraspannin (1)

Family: CD20 (1)

Homo sapiens (Human) (1)

CD20-3pp4P01

P:164-187

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (CD20_HUMAN | P11836)

molecular function
	GO:0023026	MHC class II protein complex binding	Interacting selectively and non-covalently with the class II major histocompatibility complex.
	GO:0005154	epidermal growth factor receptor binding	Interacting selectively and non-covalently with the epidermal growth factor receptor.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0042113	B cell activation	The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
	GO:0042100	B cell proliferation	The expansion of a B cell population by cell division. Follows B cell activation.
	GO:0006959	humoral immune response	An immune response mediated through a body fluid.
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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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:0005887	integral component of plasma membrane	The component of the plasma 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:154 - Pro H:155	[ RasMol ]
		Leu L:99 - Pro L:100	[ RasMol ]
		Phe H:152 - Pro H:153	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Tyr L:145 - Pro L:146	[ RasMol ]

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	3pp4
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	CD20_HUMAN \| P11836	:	1s8b 2osl 3bky

3pp3	GA101 FAB WITHOUT CD20 PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (1, 1)

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Gene Ontology (13, 13)

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