2Z93 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FAB FRAGMENT OF ANTI-CIGUATOXIN ANTIBODY 10C9 IN COMPLEX WITH CTX3C-ABCD

Authors :   M. Ui, Y. Tanaka, K. Tsumoto

Date :   14 Sep 07 (Deposition) - 06 May 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   M. Ui, Y. Tanaka, T. Tsumuraya, I. Fujii, M. Inoue, M. Hirama, K. Tsumoto
How Protein Recognizes Ladder-Like Polycyclic Ethers: Interactions Between Ciguatoxin (Ctx3C) Fragments And Its Specific Antibody 10C9
J. Biol. Chem. V. 283 19440 2008
PubMed-ID: 18463096 | Reference-DOI: 10.1074/JBC.M801282200
(for further references see the PDB file header)

Molecule 1 - ANTI-CIGUATOXIN ANTIBODY 10C9 FAB HEAVY CHAIN
	Cell Line	:	HYBRIDOMA
	Chains	:	A, C
	Engineered	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ANTI-CIGUATOXIN ANTIBODY 10C9 FAB LIGHT CHAIN
	Cell Line	:	HYBRIDOMA
	Chains	:	B, D
	Engineered	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	END	1	Ligand/Ion	1,6:5,9:8,12:11,16-TETRAANHYDRO-2,3,4,10,13,14-HEXADEOXY-D-GLYCERO-D-ALLO-D-GULO-HEPTADECA-2,13-DIENITOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	END	-1	Ligand/Ion	1,6:5,9:8,12:11,16-TETRAANHYDRO-2,3,4,10,13,14-HEXADEOXY-D-GLYCERO-D-ALLO-D-GULO-HEPTADECA-2,13-DIENITOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	END	1	Ligand/Ion	1,6:5,9:8,12:11,16-TETRAANHYDRO-2,3,4,10,13,14-HEXADEOXY-D-GLYCERO-D-ALLO-D-GULO-HEPTADECA-2,13-DIENITOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS C:35A , TRP C:47 , ASN C:58 , ASP C:95 , TRP C:103 , TYR D:36 , ARG D:46 , GLN D:89 , TRP D:91 , ASN D:94 , PRO D:96	BINDING SITE FOR RESIDUE END C 1

Asymmetric Unit

No.	Residues
1	A:140	-	A:195
2	B:134	-	B:194
3	C:22	-	C:92
4	C:140	-	C:195
5	D:23	-	D:88
6	D:134	-	D:194

Asymmetric Unit

No.	Residues
1	Phe A:146	-	Pro A:147
2	Glu A:148	-	Pro A:149
3	Phe C:146	-	Pro C:147
4	Glu C:148	-	Pro C:149
5	Trp C:188	-	Pro C:189
6	Thr D:7	-	Pro D:8
7	Asn D:94	-	Pro D:95
8	Tyr D:140	-	Pro D:141

(no "SAP(SNP)/Variant" information available for 2Z93)

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.	IGKC_MOUSE	84-90	2	B:192-197 D:193-198

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	B:192-197 -

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.	IGKC_MOUSE	84-90	1	- D:193-198

(no "Exon" information available for 2Z93)

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:81
                                                                                                                 
               SCOP domains d2z93a1 A:116-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma   SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......eeeeeeeee.....eeee....ee...eee..eeeeeeeee......eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2z93 A 116 TTPPSVYPLAPGSAVTLGCLVKGYFPEPVTVTWNSGVHTFPAVLQSDLYTLSSSVTVPSETVTCNVAHPASSTKVDKKIVP 212
                                   125   ||  141       151     ||166       176      |191       201       211 
                                       129|                  157|                 183|                       
                                        136                   163                  189

Chain B from PDB  Type:PROTEIN  Length:80
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:101
                                    13        23        33        43        53        63        73        83        93       103 
           IGKC_MOUSE     4 APTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 104
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..hhhhhhh.eeeeeee.----.....eeeee..eee...eeee..----------.eeeeeeehhhhh...eeeeee.-------.eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2z93 B 112 APTVSIFPPSSEQLTSGGASVVCFL----PKDINVKWKIDGSERQNGVLNSWT----------MSSTLTLTKDEYERHNSYTCEAT-------IVKSFNRN 212
                                   121       131    |  141       151       161  |      -   |   181       191     |   -   |   211 
                                                  136  141                    164        175                   197     205

Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------d2z93c1 C:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma       - SCOP domains
               CATH domains 2z93C01 C:3-113 Immunoglobulins                                                                                   2z93C02 C:114-213 Immunoglobulins                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...ee.....eeeeeee.........eeeeeee.....eeeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee....eee...eeeee........eeeee....eeeeeee.....eeee........eee...ee....eeeeeee........eeeeeeehhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z93 C   3 QLLESGPDLVKPSQSLSLTCTVTGYSITSGYNWHWIRQFPGNKLEWMGYIHYRGTTNYNTSLKSRISITRDSSKNQFFLQLNSVTTEDTATYYCACDDFYSDYWGQGTIVTVSSAKTTPPSVYPLAPTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTWPSETVTCNVAHPASSTKVDKKIVPR 213
                                    12        22        32   |    41        51        61        71        81 |||    88        98||     109       119      |139       149       159       169       179   ||  192       202       212 
                                                           35A                                             82A||               99|                      126|                                           183|                          
                                                                                                            82B|               101                       137                                            187                          
                                                                                                             82C

Chain D from PDB  Type:PROTEIN  Length:184
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:204
                                                                                                                                       1                                                                                                
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        93    
           IGKC_MOUSE     - -----------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPI  97
               SCOP domains d2z93d1 D:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                d2z93d2 D:108-205 Immunoglobulin light cha       in kappa constant domai             n, CL-kappa   SCOP domains
               CATH domains 2z93D01 D:1-108 Immunoglobulins                                                                            2z93D02 D:109-205 Immunoglobulins                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeee............eeeee.......eeeee....hhhhhh...eeeeeeee.....eeee.-------...eeee.........eeeeeee-------------.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z93 D   1 ELVMTQTPAIMSASPGEKVTMTCSASSSVSSVHWYQQKSGTSPKRWIYDTSKLPSGVPGRFSGSGSGTSYSLTISSMEAEDAATYYCQQWSSNPPTFGAGTKLEVKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWK-------NGVLNSWTDQDSKDSTYSMSSTL-------------TCEATHKTSTSPI 205
                                    10        20      ||31        41        51        61        71        81        91       101       111       121       131       141       | -     | 161       171       | -         - |     201    
                                                     27|                                                                                                                     149     157                   179           193            
                                                      29

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)

Mouse (Mus musculus) (152)

1a	2z93D02	D:109-205
1b	2z93D01	D:1-108
1c	2z93C02	C:114-213
1d	2z93C01	C:3-113

(no "Pfam Domain" information available for 2Z93)

Asymmetric Unit(hide GO term definitions)

Chain B,D (IGKC_MOUSE | P01837)

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:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	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.
	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 Unit
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	Cis Peptide Bonds
		Asn D:94 - Pro D:95	[ RasMol ]
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu C:148 - Pro C:149	[ RasMol ]
		Phe A:146 - Pro A:147	[ RasMol ]
		Phe C:146 - Pro C:147	[ RasMol ]
		Thr D:7 - Pro D:8	[ RasMol ]
		Trp C:188 - Pro C:189	[ RasMol ]
		Tyr D:140 - Pro D:141	[ RasMol ]

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	2z93
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2z91	CRYSTAL STRUCTURE OF THE SAME PROTEIN WITHOUT LIGAND MOLECULE
2z92	CRYSTAL STRUCTURE OF THE SAME PROTEIN IN COMPLEX WITH CTX3C -ABCDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (6, 6)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 4)

CATH Domains (1, 4)

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Gene Ontology (14, 14)

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