1A6V - JenaLib

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Title :   B1-8 FV FRAGMENT COMPLEXED WITH A (4-HYDROXY-3-NITROPHENYL) ACETATE COMPOUND

Authors :   T. Simon, K. Henrick, M. Hirshberg, G. Winter

Date :   03 Mar 98 (Deposition) - 15 Jul 98 (Release) - 14 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : H,I,J,L,M,N
Biol. Unit 1: H,L  (1x)
Biol. Unit 2: I,M  (1x)
Biol. Unit 3: J,N  (1x)

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

Reference :   T. Simon, K. Henrick, M. Hirshberg, G. Winter
X-Ray Structures Of Fv Fragment And Its (4-Hydroxy-3-Nitrophenyl)Acetate Complex Of Murine B1-8 Antibody
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - B1-8 FV (LIGHT CHAIN)
	Cell Line	:	J558L
	Chains	:	L, M, N
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	J558L
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Expression System Vector	:	PEC-GAMMA3
	Fragment	:	FV FRAGMENT
	Organ	:	TAIL
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	C57BL/6

Molecule 2 - B1-8 FV (HEAVY CHAIN)
	Cell Line	:	J558L
	Chains	:	H, I, J
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cell Line	:	J558L
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Expression System Vector	:	PEC-GAMMA3
	Fragment	:	FV FRAGMENT
	Organ	:	TAIL
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	C57BL/6

		1	2	3	4	5	6
Asymmetric Unit	:	H	I	J	L	M	N
Biological Unit 1 (1x)	:	H			L
Biological Unit 2 (1x)	:		I			M
Biological Unit 3 (1x)	:			J			N

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NPC	3	Ligand/Ion	4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	NPC	3	Ligand/Ion	4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NPC	-1	Ligand/Ion	4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NPC	-1	Ligand/Ion	4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROIC ACIDANION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	unknown	HOH H:73 , TRP H:333 , HIS H:335 , ARG H:350 , LYS H:359 , TYR H:401 , SER H:405 , TYR L:34 , TRP L:93 , TRP L:98	NULL
2	AC2	unknown	HOH H:73 , HOH H:141 , TRP H:333 , HIS H:335 , ARG H:350 , LYS H:359 , TYR H:399 , TYR H:401 , NPC H:430 , TRP L:93 , TRP L:98	NULL
3	AC3	unknown	TRP I:333 , HIS I:335 , ARG I:350 , LYS I:359 , TYR I:399 , TYR I:401 , TYR I:402 , SER I:405 , HOH I:512 , HOH I:513 , TYR M:34 , TRP M:93 , TRP M:98	NULL
4	AC4	unknown	TRP J:333 , HIS J:335 , ARG J:350 , LYS J:359 , TYR J:399 , TYR J:401 , HOH J:437 , HOH J:514 , THR N:31 , SER N:32 , TYR N:34 , TRP N:93	NULL

Asymmetric Unit

No.	Residues
1	H:322	-	H:396
2	I:322	-	I:396
3	J:322	-	J:396
4	L:22	-	L:90
5	M:22	-	M:90
6	N:22	-	N:90

(no "Cis Peptide Bond" information available for 1A6V)

(no "SAP(SNP)/Variant" information available for 1A6V)

(no "PROSITE Motif" information available for 1A6V)

(no "Exon" information available for 1A6V)

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:118
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:118
                                    29        39        49        59        69        79        89        99       109       119       129        
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTV 137
               SCOP domains d1a6vh_ H: Immunoglobulin heavy chain variable domain, VH                                                              SCOP domains
               CATH domains 1a6vH00 H:301-418 Immunoglobulins                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee......eeeeeeee...hhh.eeeeeee......eeeeeee....eeee.hhh...eeeeee....eeeeee........eeeeeeee..............eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v H 301 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTV 418
                                   310       320       330       340       350       360       370       380       390       400       410

Chain I from PDB  Type:PROTEIN  Length:119
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:119
                                    29        39        49        59        69        79        89        99       109       119       129         
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVS 138
               SCOP domains d1a6vi_ I: Immunoglobulin heavy chain variable domain, VH                                                               SCOP domains
               CATH domains 1a6vI00 I:301-419 Immunoglobulins                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee.......eeeeeee.....eeeeeeee.....eee.hhh...eeeeee....eeeeee........eeeeeeee.......eeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v I 301 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVS 419
                                   310       320       330       340       350       360       370       380       390       400       410

Chain J from PDB  Type:PROTEIN  Length:120
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:120
                                    29        39        49        59        69        79        89        99       109       119       129       139
          HVM07_MOUSE    20 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS 139
               SCOP domains d1a6vj_ J: Immunoglobulin heavy chain variable domain, VH                                                                SCOP domains
               CATH domains 1a6vJ00 J:301-420 Immunoglobulins                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eee..........eeee.......eeeeeee.....eeeeee.....................................hhh.eeeeeeee.......eeee...eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1a6v J 301 QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVSS 420
                                   310       320       330       340       350       360       370       380       390       400       410       420

Chain L from PDB  Type:PROTEIN  Length:110
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:110
                                    29        39        49        59        69        79        89        99       109       119       129
           LV1B_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLG 129
               SCOP domains d1a6vl_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                        SCOP domains
               CATH domains 1a6vL00 L:1-110 Immunoglobulins                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eee.....eeeeeeee...........eeeeee...eeeeee.............eeeeee..eeeeeee...hhh.eeeeeeeee..eeee...eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v L   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLE 110
                                    10        20        30        40        50        60        70        80        90       100       110

Chain M from PDB  Type:PROTEIN  Length:109
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:109
                                    29        39        49        59        69        79        89        99       109       119         
           LV1B_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1a6vm_ M: Immunoglobulin light chain lambda variable domain, VL-lambda                                       SCOP domains
               CATH domains 1a6vM00 M:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeee........hhh..eeeeee...eeeeee.............eeeeee..eeeeee........eeeeeeee....eee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v M   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 109
                                    10        20        30        40        50        60        70        80        90       100

Chain N from PDB  Type:PROTEIN  Length:109
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:109
                                    29        39        49        59        69        79        89        99       109       119         
           LV1B_MOUSE    20 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1a6vn_ N: Immunoglobulin light chain lambda variable domain, VL-lambda                                       SCOP domains
               CATH domains 1a6vN00 N:1-109 Immunoglobulins                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee....eeeeee............eeeeee...eeeeee.............eeeeee..eeeeee........eeeeeeeee..eeee...eeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1a6v N   1 QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 109
                                    10        20        30        40        50        60        70        80        90       100

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)

House mouse (Mus musculus) (616)

1a	1a6vH00	H:301-418
1b	1a6vM00	M:1-109
1c	1a6vN00	N:1-109
1d	1a6vL00	L:1-110
1e	1a6vI00	I:301-419
1f	1a6vJ00	J:301-420

(no "Pfam Domain" information available for 1A6V)

Asymmetric Unit(hide GO term definitions)

Chain H,I,J (HVM07_MOUSE | P01751)

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.

Chain L,M,N (LV1B_MOUSE | P01724)

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.

Asymmetric Unit
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	1a6v
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(no "Related Entries Specified in the PDB File" available for 1A6V)

Description

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Ligands, Modified Residues, Ions (1, 3)

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SS Bonds (6, 6)

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