1C5D - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A RAT MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR

Authors :   M. Kontou, D. D. Leonidas, E. H. Vatzaki, P. Tsantili, A. Mamalaki, N. G. Oikonomakos, K. R. Acharya, S. J. Tzartos

Date :   17 Nov 99 (Deposition) - 03 Dec 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,H,L
Biol. Unit 1: A,B,H,L  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: H,L  (1x)

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

Reference :   M. Kontou, D. D. Leonidas, E. H. Vatzaki, P. Tsantili, A. Mamalaki, N. G. Oikonomakos, K. R. Acharya, S. J. Tzartos
The Crystal Structure Of The Fab Fragment Of A Rat Monoclonal Antibody Against The Main Immunogenic Region Of The Human Muscle Acetylcholine Receptor.
Eur. J. Biochem. V. 267 2389 2000
PubMed-ID: 10759865 | Reference-DOI: 10.1046/J.1432-1327.2000.01252.X

Molecule 1 - MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
	Chains	:	L, A
	Fragment	:	FAB FRAGMENT, HEAVY CHAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

Molecule 2 - MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
	Chains	:	H, B
	Fragment	:	FAB FRAGMENT, LIGHT CHAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:	A	B	H	L
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1C5D)

(no "Site" information available for 1C5D)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:133	-	A:193
3	A:213	-	B:132
4	B:22	-	B:95
5	B:144	-	B:197
6	H:22	-	H:95
7	H:144	-	H:197
8	L:23	-	L:88
9	L:133	-	L:193
10	L:213	-	H:132

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Tyr L:139	-	Pro L:140
3	Phe H:150	-	Pro H:151
4	Glu H:152	-	Pro H:153
5	Trp H:190	-	Pro H:191
6	Tyr A:139	-	Pro A:140
7	Phe B:150	-	Pro B:151
8	Glu B:152	-	Pro B:153
9	Trp B:190	-	Pro B:191

(no "SAP(SNP)/Variant" information available for 1C5D)

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:191-197 L:191-197

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:191-197 L:191-197

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	A:191-197 -

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	- L:191-197

(no "Exon" information available for 1C5D)

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:213
 aligned with KACB_RAT | P01835 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:213
                                                                                                                                       1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103   
             KACB_RAT     - -----------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC 106
               SCOP domains d1c5da1 A:1-106 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1c5da2 A:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1c5dA01 A:1-107 Immunoglobulins                                                                            1c5dA02 A:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeee...eeeeeeee.......eeeeee......eeee.............eeeeee..eeeeeee...hhh..eeeeee...........eeeee......eeeee...hhhhh..eeeeeeeee..........eee..eee...eeeee...........eeeeeeee..hhhh.......................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5d A   1 DIQMTQSPPSLSASLGDKVTITCQASQDINKYIAWYQQKPGKAPRQLIRYTSILVLGTPSRFSGSGSGRDFSFSISNVASEDIASYYCLQYGNLYTFGAGTKLEIKRADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1c5db1 B:1-117 Immunoglobulin heavy chain variable domain, VH                                                       d1c5db2 B:118-215 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 1c5dB01 B:1-117 Immunoglobulins                                                                                      1c5dB02 B:118-214 Immunoglobulins                                                                - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........eeeeeee.........eeeeeee....eeeeeee.....eee.......eeeeee....eeeeee....hhh.eeeeeee.............eee..........eeeee...........eeeeeeeeee.....eeee..............eee..eeeeeeeeee........eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5d B   1 EVKLLESGPGLVQPSQTLSLTCTVSGFPLTTNGVSWVRQPPGKGLEWIAAISSGGSPYYNSALKSRLSINRDTSKSQVFLKMNSLQTEDTAIYFCTREDGWNYFDYWGPGTMVTVSSAQTTAPSVYPLAPGCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGALSSDVHTFPAVLQSGLYTLTSSVTSSTWPSQTVTCNVAHPASSTKVDKKLERR 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d1c5dh1 H:1-117 Immunoglobulin heavy chain variable domain, VH                                                       d1c5dh2 H:118-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                   SCOP domains
               CATH domains 1c5dH01 H:1-117 Immunoglobulins                                                                                      1c5dH02 H:118-214 Immunoglobulins                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........eeeeeee.........eeeeee.....eeeeeee............hhheeeeee....eeeeee....hhh.eeeeeee.............eee..........eeeee...........eeeeeeee.......eeeehhh...........eee..eeeeeeeeee........eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5d H   1 EVKLLESGPGLVQPSQTLSLTCTVSGFPLTTNGVSWVRQPPGKGLEWIAAISSGGSPYYNSALKSRLSINRDTSKSQVFLKMNSLQTEDTAIYFCTREDGWNYFDYWGPGTMVTVSSAQTTAPSVYPLAPGCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGALSSDVHTFPAVLQSGLYTLTSSVTSSTWPSQTVTCNVAHPASSTKVDKKLER 214
                                    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:213
 aligned with KACB_RAT | P01835 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:213
                                                                                                                                       1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93       103   
             KACB_RAT     - -----------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC 106
               SCOP domains d1c5dl1 L:1-106 Immunoglobulin light chain kappa variable domain, VL-kappa                                d1c5dl2 L:107-213 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1c5dL01 L:1-107 Immunoglobulins                                                                            1c5dL02 L:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.......eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee..........eeeeee......eeeee...hhhhhh.eeeeeeeee..........eee..eee...eeeee...........eeeeeeeehhhhhh..eee..............eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c5d L   1 DIQMTQSPPSLSASLGDKVTITCQASQDINKYIAWYQQKPGKAPRQLIRYTSILVLGTPSRFSGSGSGRDFSFSISNVASEDIASYYCLQYGNLYTFGAGTKLEIKRADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC 213
                                    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 '\|'

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	1c5dA02	A:108-210
1b	1c5dL02	L:108-210
1c	1c5dA01	A:1-107
1d	1c5dL01	L:1-107
1e	1c5dB02	B:118-214
1f	1c5dH02	H:118-214
1g	1c5dB01	B:1-117
1h	1c5dH01	H:1-117

(no "Pfam Domain" information available for 1C5D)

Asymmetric Unit(hide GO term definitions)

Chain A,L (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 1c5d)

	Sites
(no "Sites" information available for 1c5d)

	Cis Peptide Bonds
		Glu B:152 - Pro B:153	[ RasMol ]
		Glu H:152 - Pro H:153	[ RasMol ]
		Phe B:150 - Pro B:151	[ RasMol ]
		Phe H:150 - Pro H:151	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp B:190 - Pro B:191	[ RasMol ]
		Trp H:190 - Pro H:191	[ RasMol ]
		Tyr A:139 - Pro A:140	[ RasMol ]
		Tyr L:139 - Pro L:140	[ RasMol ]

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