1FN4 - JenaLib

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Title :   CRYSTAL STRUCTURE OF FAB198, AN EFFICIENT PROTECTOR OF ACETYLCHOLINE RECEPTOR AGAINST MYASTHENOGENIC ANTIBODIES

Authors :   K. Poulas, E. Eliopoulos, E. Vatzaki, J. Navaza, M. Kontou

Date :   21 Aug 00 (Deposition) - 26 Sep 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Fab198, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Poulas, E. Eliopoulos, E. Vatzaki, J. Navaza, M. Kontou, N. Oikonomakos, K. R. Acharya, S. J. Tzartos
Crystal Structure Of Fab198, An Efficient Protector Of The Acetylcholine Receptor Against Myasthenogenic Antibodies.
Eur. J. Biochem. V. 268 3685 2001
PubMed-ID: 11432734 | Reference-DOI: 10.1046/J.1432-1327.2001.02274.X

Molecule 1 - MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR
	Chains	:	A, C
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

Molecule 2 - MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR
	Chains	:	B, D
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1FN4)

(no "Site" information available for 1FN4)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:131	-	A:191
3	A:211	-	B:208
4	B:22	-	B:92
5	B:133	-	B:188
6	C:23	-	C:88
7	C:131	-	C:191
8	C:211	-	D:208
9	D:22	-	D:92
10	D:133	-	D:188

Asymmetric Unit

No.	Residues
1	Tyr C:137	-	Pro C:138
2	Phe D:139	-	Pro D:140
3	Glu D:141	-	Pro D:142

(no "SAP(SNP)/Variant" information available for 1FN4)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	KACB_RAT	84-90	2	A:189-195 C:189-195

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	KACB_RAT	84-90	2	A:189-195 C:189-195

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	KACB_RAT	84-90	1	- C:189-195

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	KACB_RAT	84-90	1	A:189-195 -

(no "Exon" information available for 1FN4)

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 A from PDB  Type:PROTEIN  Length:211
 aligned with KACB_RAT | P01835 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:211
                                                                                                                                     1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -     |   5        15        25        35        45        55        65        75        85        95       105 
            KACB_RAT      - ---------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC  106
               SCOP domains d1fn4a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1fn4a2 A:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1fn4A01 A:1-107 Immunoglobulins                                                                            1fn4A02 A:108-208 Immunoglobulins                                                                    --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eee......eeeeeee.......eeeee.......eeee.................ee..eeeeee.........eeeeee..........eeee.............hhhhhh..eeeeee............ee..........eeee.............eeeeeee...........ee..........ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fn4 A    1 DIKLTQSPSLLSASVGDRVTLSCKGSQNINNYLAWYQQKLGEAPKLLIYNTNSLQTGIPSRFSGSGSGTDYTLTISSLQPEDVATYFCYQYNNGYTFGAGTKLELKRTAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC  211
                                    10        20        30        40        50        60        70        80        90   ||  101     | 110       120       130       140       150       160       170       180       190       200       210 
                                                                                                                        94|       106A                                                                                                         
                                                                                                                         96

Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1fn4b1 B:1-106 Immunoglobulin heavy chain variable domain, VH                                                      d1fn4b2 B:107-208 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1fn4B01 B:1-106 Immunoglobulins                                                                                     1fn4B02 B:107-205 Immunoglobulins                                                                  --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.........ee..eee.........eeeeeeee.....eeeeee.....eeehhhhhh....ee.hhh.eee...........eeeeeeee........................eeeee.............eeeeee..........hhhhh..........ee....ee..eee.................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fn4 B    1 QVQLLESGPGLVRPSETLSLTCTVSGFSLTSFSVSWVRHPSGKGPEWMGRMWYDGYTAYNSALKSRLSISRDTSKNQVFLKMNSLQTDDTGTYYCTRDLYGGYPLGFWYFDFWGPGTMVTVSSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWSSQAVTCNVAHPASSTKVDKKIVPRDC  208
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G       110       120       130       140       150       160       170       180       190       200        
                                                                                                            82A||               100A||||||                                                                                                            
                                                                                                             82B|                100B|||||                                                                                                            
                                                                                                              82C                 100C||||                                                                                                            
                                                                                                                                   100D|||                                                                                                            
                                                                                                                                    100E||                                                                                                            
                                                                                                                                     100F|                                                                                                            
                                                                                                                                      100G

Chain C from PDB  Type:PROTEIN  Length:211
 aligned with KACB_RAT | P01835 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:211
                                                                                                                                     1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -     |   5        15        25        35        45        55        65        75        85        95       105 
            KACB_RAT      - ---------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC  106
               SCOP domains d1fn4c1 C:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1fn4c2 C:108-211 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1fn4C01 C:1-107 Immunoglobulins                                                                            1fn4C02 C:108-208 Immunoglobulins                                                                    --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eee.....eeeeeeee.......eeeee.......eeeee...ee.........eeee..eeeeeee.......eeeeeee..........eeee.......eeee..hhhhhh..eeeeeeeeeee.......eeee........eee...........eeeeeeeeeehhhhhh...eeee..........ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fn4 C    1 DIKLTQSPSLLSASVGDRVTLSCKGSQNINNYLAWYQQKLGEAPKLLIYNTNSLQTGIPSRFSGSGSGTDYTLTISSLQPEDVATYFCYQYNNGYTFGAGTKLELKRTAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC  211
                                    10        20        30        40        50        60        70        80        90   ||  101     | 110       120       130       140       150       160       170       180       190       200       210 
                                                                                                                        94|       106A                                                                                                         
                                                                                                                         96

Chain D from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1fn4d1 D:1-106 Immunoglobulin heavy chain variable domain, VH                                                      d1fn4d2 D:107-208 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1fn4D01 D:1-106 Immunoglobulins                                                                                     1fn4D02 D:107-205 Immunoglobulins                                                                  --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeeeeee.......eeeeee.......eeeeee.....eeehhhhhh.eeeeee....................eeeeee........................eeeee..........eeeeeeeeeee........hhhhh.....ee...ee....eee.eeeeeehhhhh....eee...hhhh...eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1fn4 D    1 QVQLLESGPGLVRPSETLSLTCTVSGFSLTSFSVSWVRHPSGKGPEWMGRMWYDGYTAYNSALKSRLSISRDTSKNQVFLKMNSLQTDDTGTYYCTRDLYGGYPLGFWYFDFWGPGTMVTVSSVFPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWSSQAVTCNVAHPASSTKVDKKIVPRDC  208
                                    10        20        30        40        50        60        70        80  |||   87        97   |||100G       110       120       130       140       150       160       170       180       190       200        
                                                                                                            82A||               100A||||||                                                                                                            
                                                                                                             82B|                100B|||||                                                                                                            
                                                                                                              82C                 100C||||                                                                                                            
                                                                                                                                   100D|||                                                                                                            
                                                                                                                                    100E||                                                                                                            
                                                                                                                                     100F|                                                                                                            
                                                                                                                                      100G

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Norway rat (Rattus norvegicus) (32)

1a	1fn4A02	A:108-208
1b	1fn4C02	C:108-208
1c	1fn4A01	A:1-107
1d	1fn4C01	C:1-107
1e	1fn4B02	B:107-205
1f	1fn4D02	D:107-205
1g	1fn4B01	B:1-106
1h	1fn4D01	D:1-106

(no "Pfam Domain" information available for 1FN4)

Asymmetric Unit(hide GO term definitions)

Chain A,C (KACB_RAT | P01835)

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.

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(no "Ligands, Modified Residues, Ions" information available for 1fn4)

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	Cis Peptide Bonds
		Glu D:141 - Pro D:142	[ RasMol ]
		Phe D:139 - Pro D:140	[ RasMol ]
		Tyr C:137 - Pro C:138	[ RasMol ]

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	1fn4
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(no "Related Entries Specified in the PDB File" available for 1FN4)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (10, 10)

Cis Peptide Bonds (3, 3)

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