1OAY - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   ANTIBODY MULTISPECIFICITY MEDIATED BY CONFORMATIONAL DIVERSITY

Authors :   L. C. James, P. Roversi, D. Tawfik

Date :   21 Jan 03 (Deposition) - 15 Jan 04 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.66

Chains :   Asym. Unit : H,J,L,M,N,O
Biol. Unit 1: H,L  (1x)
Biol. Unit 2: M  (1x)
Biol. Unit 3: J,N  (1x)
Biol. Unit 4: O  (1x)

Keywords :   Immune System, Antibody/Complex, Antibody, Allergy, Ige, Conformational Diversity, Multispecificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. C. James, P. Roversi, D. Tawfik
Antibody Multispecificity Mediated By Conformational Diversity
Science V. 299 1362 2003
PubMed-ID: 12610298 | Reference-DOI: 10.1126/SCIENCE.1079731

Molecule 1 - IMMUNOGLOBULIN E
	Chains	:	H, I, J, K
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FV REGION, RESIDUES 1-122
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	EXPRESSED AS RECOMBINANT FV IN E.COLI

Molecule 2 - IMMUNOGLOBULIN E
	Chains	:	L, M, N, O
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FV REGION, RESIDUES 1-110
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	EXPRESSED AS RECOMBINANT FV IN E.COLI

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FUR	2	Ligand/Ion	FURAZOLIDONE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	FUR	1	Ligand/Ion	FURAZOLIDONE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	FUR	-1	Ligand/Ion	FURAZOLIDONE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	FUR	1	Ligand/Ion	FURAZOLIDONE

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	FUR	-1	Ligand/Ion	FURAZOLIDONE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP H:33 , HIS H:35 , LYS H:59 , MET H:99 , HOH H:2080 , ASN L:36 , TRP L:93 , LEU L:98 , LEU O:68	BINDING SITE FOR RESIDUE FUR H 500
2	AC2	SOFTWARE	TRP J:33 , HIS J:35 , LYS J:59 , LEU M:68 , ASN N:36 , TRP N:93 , LEU N:98	BINDING SITE FOR RESIDUE FUR J 500

Asymmetric Unit

No.	Residues
1	H:22	-	H:96
2	J:22	-	J:96
3	L:22	-	L:90
4	M:22	-	M:90
5	N:22	-	N:90
6	O:22	-	O:90

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

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

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

(no "Exon" information available for 1OAY)

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:121
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:121
                                                                                                                                                139  
                                    30        40        50        60        70        80        90       100       110       120       130        |- 
          HVM07_MOUSE    21 VQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS--   -
               SCOP domains d1oayh_ H: Immunoglobulin heavy chain variable domain, VH                                                                 SCOP domains
               CATH domains 1oayH00 H:2-122 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eee.eeee..hhhhheeeeeee.......eeeeee....eeee.........eeee....eeeeee...hhhhh.eeeeeeee.....eeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oay H   2 VQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNLKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSSAA 122
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain J from PDB  Type:PROTEIN  Length:121
 aligned with HVM07_MOUSE | P01751 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:121
                                                                                                                                                139  
                                    30        40        50        60        70        80        90       100       110       120       130        |- 
          HVM07_MOUSE    21 VQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTLTVSS--   -
               SCOP domains d1oayj_ J: Immunoglobulin heavy chain variable domain, VH                                                                 SCOP domains
               CATH domains 1oayJ00 J:2-122 Immunoglobulins                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eee.eeee..hhhhheeeeeee......eeeeeee....eeee.........eeee....eeeeee...hhhhh.eeeeeeee.....eeeee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oay J   2 VQLQQSGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNGGGTKYNLKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARMWYYGTYYFDYWGQGTTLTVSSAA 122
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain L from PDB  Type:PROTEIN  Length:108
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:108
                                    30        40        50        60        70        80        90       100       110       120        
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oayl_ L: Immunoglobulin light chain lambda variable domain, VL-lambda                                      SCOP domains
               CATH domains 1oayL00 L:2-109 Immunoglobulins                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee.......eeeee.............eeeeee...eeeeeee...ee.......eeeeee..eeeeee.........eeeeeee....eee....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oay L   2 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPRHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                                    11        21        31        41        51        61        71        81        91       101

Chain M from PDB  Type:PROTEIN  Length:85
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:103
                                    30        40        50        60        70        80        90       100       110       120   
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGT 123
               SCOP domains d1oaym_ M: Immunoglobulin  li    ght chain lambda    va   riable domain, VL-lambda                      SCOP domains
               CATH domains 1oayM00 M:2-104 Immunoglo bul    ins                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee........-...----.eeeee.......eee---...---....eeeeee..eeeeeee........eeeee-------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1oay M   2 AVVTQESALTTSPGETVTLTCRSST-AVT----ANWVQEKPRHLFTGLI---NNR---VPARFSGSLIGNKAALTITGAQTEDEAIYFCA-------VFGGGT 104
                                    11        21    | | |-   |    41        |-  | |   61        71        81        91       101   
                                                   26 | |   35             50  54 |  60                             91      99     
                                                     28 |                        56                                                
                                                       30

Chain N from PDB  Type:PROTEIN  Length:107
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:108
                                    30        40        50        60        70        80        90       100       110       120        
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oa yn_ N: Immunoglobulin light chain lambda variable domain, VL-lambda                                     SCOP domains
               CATH domains 1oay N00 N:2-109 Immunoglobulins                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee-..eeee.....eeeeeee...........eeeeee...eeeeeee...ee.......eeeeee..eeeeee.........eeeeeee....eee....eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oay N   2 AVVT-ESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPRHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHLVFGGGTKLTVL 109
                               | |  11        21        31        41        51        61        71        81        91       101        
                               5 7

Chain O from PDB  Type:PROTEIN  Length:92
 aligned with LV1B_MOUSE | P01724 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:108
                                    30        40        50        60        70        80        90       100       110       120        
           LV1B_MOUSE    21 AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQQKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVL 128
               SCOP domains d1oayo_ O: Immunoglobulin  li     ght chain lambda varia   ble domain, VL-lambda                             SCOP domains
               CATH domains 1oayO00 O:2-109 Immunoglo bul     ins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............ee........-...-----..eee.................---...eeeeee..eeeeeee........eee..-------........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1oay O   2 AVVTQESALTTSPGETVTLTCRSST-AVT-----NWVQEKPRHLFTGLIGGTNNRA---PARFSGSLIGNKAALTITGAQTEDEAIYFCA-------VFGGGTKLTVL 109
                                    11        21    | | |-    |   41        51     |  61        71        81        91       101        
                                                   26 | |    36                   57  61                            91      99          
                                                     28 |                                                                               
                                                       30

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)

Black rat, roof rat (Rattus rattus) (7)

1a	1oayH00	H:2-122
1b	1oayJ00	J:2-122
1c	1oayN00	N:2-109
1d	1oayL00	L:2-109
1e	1oayO00	O:2-109
1f	1oayM00	M:2-104

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

Asymmetric Unit(hide GO term definitions)

Chain H,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,O (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.

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	1oay
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	LV1B_MOUSE \| P01724
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1oaq	FREE CONFORMATION AB1 OF THE IGE SPE-7
1oar	FV IGE SPE-7 IN COMPLEX WITH ALIZARIN RED
1oau	FV STRUCTURE OF THE IGE SPE-7 IN COMPLEX WITH DNP-SER (IMMUNISING HAPTEN)
1oax	FV STRUCTURE OF THE IGE SPE-7 IN COMPLEX WITH ACENAPHTHENEQUINONE
1oaz	IGE FV SPE7 COMPLEXED WITH A RECOMBINANT THIOREDOXIN

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (6, 6)

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