3CFD - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PURPLE-FLUORESCENT ANTIBODY EP2-25C10 IN COMPLEX WITH ITS STILBENE HAPTEN

Authors :   E. W. Debler, A. Heine, I. A. Wilson

Date :   03 Mar 08 (Deposition) - 18 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Immunoglobulin, Purple-Fluorescent Antibody, Hapten Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. W. Debler, G. F. Kaufmann, M. M. Meijler, A. Heine, J. M. Mee, G. Pljevaljcic, A. J. Di Bilio, P. G. Schultz, D. P. Millar, K. D. Janda I. A. Wilson, H. B. Gray, R. A. Lerner
Deeply Inverted Electron-Hole Recombination In A Luminescen Antibody-Stilbene Complex.
Science V. 319 1232 2008
PubMed-ID: 18309081 | Reference-DOI: 10.1126/SCIENCE.1153445

Molecule 1 - PURPLE-FLUORESCENT ANTIBODY EP2-25C10-KAPPA LIGHT CHAIN
	Cell	:	HYBRIDOMA CELLS FROM 129GIX+ SPLEEN CELLS FUSED WITH BALB/C MYELOMA CELLS
	Chains	:	L, A
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	PURIFIED FROM ASCITIC FLUID

Molecule 2 - PURPLE-FLUORESCENT ANTIBODY EP2-25C10-IGG2B HEAVY CHAIN
	Cell	:	HYBRIDOMA CELLS FROM 129GIX+ SPLEEN CELLS FUSED WITH BALB/C MYELOMA CELLS
	Chains	:	H, B
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	PURIFIED FROM ASCITIC FLUID

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SPB	2	Ligand/Ion	4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SPB	1	Ligand/Ion	4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SPB	1	Ligand/Ion	4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN H:35A , TYR H:50 , ARG H:58 , SER H:95 , GLY H:98 , GLY H:100A , TRP H:103 , TYR L:36 , GLN L:89 , THR L:93 , LEU L:94 , PRO L:96 , PHE L:98	BINDING SITE FOR RESIDUE SPB H 301
2	AC2	SOFTWARE	TYR A:36 , GLN A:89 , THR A:93 , LEU A:94 , PRO A:96 , PHE A:98 , ASN B:35A , TYR B:50 , SER B:95 , GLY B:98 , GLY B:100A , TRP B:103	BINDING SITE FOR RESIDUE SPB B 302
3	AC3	SOFTWARE	ARG H:71 , ASP L:151 , HIS L:189	BINDING SITE FOR RESIDUE GOL H 401

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:142	-	B:208
5	H:22	-	H:92
6	H:142	-	H:208
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Leu L:94	-	Pro L:95
2	Tyr L:140	-	Pro L:141
3	Phe H:148	-	Pro H:149
4	Glu H:150	-	Ser H:151
5	Trp H:199	-	Pro H:200
6	Leu A:94	-	Pro A:95
7	Tyr A:140	-	Pro A:141
8	Phe B:148	-	Pro B:149
9	Glu B:150	-	Ser B:151
10	Trp B:199	-	Pro B:200

(no "SAP(SNP)/Variant" information available for 3CFD)

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	A:192-198 L:192-198

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	A:192-198 -

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	- L:192-198

(no "Exon" information available for 3CFD)

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 IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:213
                                                                                                                                        1                                                                                                        
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102   
          IGKC_MOUSE      - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  105
               SCOP domains d3cfda1 A:1-107 automated matches                                                                          d3cfda2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains 3cfdA01 A:1-107 Immunoglobulins                                                                            3cfdA02 A:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3cfd A    1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLDQDDIATYFCQQGTTLPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  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:219
                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cfdB01 B:1-113 Immunoglobulins                                                                                         3cfdB02 B:114-227 Immunoglobulins                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee...eeeeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeeee......eeeeeeeeee..eeeeeeeeeee.........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3cfd B    1 EVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWLRQLPGNKLEWMGYISYSGRIRYNPSLKRRISITRDTSKNQFFLQLNSVTTEDTATYYCARSDYGNYGRGDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTSGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEP  227
                                    10        20        30     |  39        49        59        69        79   |||  86        96    |||103       113       123      |135       145       156||     171       183       193  || ||205||     216      || 
                                                             35A                                             82A||               100A||                           130|                  154|||    169|      180|          196| || 206|            223| 
                                                                                                              82B|                100B|                            133                   156||     171       183           198 ||  208             226 
                                                                                                               82C                 100C                                                   157|                               200|                      
                                                                                                                                                                                           162                                202

Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cfdH01 H:1-113 Immunoglobulins                                                                                         3cfdH02 H:114-228 Immunoglobulins                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeee.......eeee...eeeee........eeeee..........eeeeeeeeeee.....eeeee......eeeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3cfd H    1 EVQLQESGPGLVKPSQSLSLTCTVTGYSITSDYAWNWLRQLPGNKLEWMGYISYSGRIRYNPSLKRRISITRDTSKNQFFLQLNSVTTEDTATYYCARSDYGNYGRGDYWGQGTSVTVSSAKTTPPSVYPLAPGCGDTTGSSVTSGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSETVTCSVAHPASSTTVDKKLEPS  228
                                    10        20        30     |  39        49        59        69        79   |||  86        96    |||103       113       123      |135       145       156||     171       183       193  || ||205||     216      |228
                                                             35A                                             82A||               100A||                           130|                  154|||    169|      180|          196| || 206|            223|  
                                                                                                              82B|                100B|                            133                   156||     171       183           198 ||  208             226  
                                                                                                               82C                 100C                                                   157|                               200|                       
                                                                                                                                                                                           162                                202

Chain L from PDB  Type:PROTEIN  Length:213
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:213
                                                                                                                                        1                                                                                                        
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102   
          IGKC_MOUSE      - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  105
               SCOP domains d3cfdl1 L:1-107 automated matches                                                                          d3cfdl2 L:108-213 automated matches                                                                        SCOP domains
               CATH domains 3cfdL01 L:1-107 Immunoglobulins                                                                            3cfdL02 L:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee.......eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3cfd L    1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLDQDDIATYFCQQGTTLPPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d3cfda1	A:1-107
1b	d3cfdl1	L:1-107

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

2a	d3cfda2	A:108-213
2b	d3cfdl2	L:108-213

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	3cfdA02	A:108-211
1b	3cfdH02	H:114-228
1c	3cfdB02	B:114-227
1d	3cfdB01	B:1-113
1e	3cfdH01	H:1-113
1f	3cfdL02	L:108-211
1g	3cfdA01	A:1-107
1h	3cfdL01	L:1-107

(no "Pfam Domain" information available for 3CFD)

Asymmetric Unit(hide GO term definitions)

Chain A,L (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
		Glu B:150 - Ser B:151	[ RasMol ]
		Glu H:150 - Ser H:151	[ RasMol ]
		Leu A:94 - Pro A:95	[ RasMol ]
		Leu L:94 - Pro L:95	[ RasMol ]
		Phe B:148 - Pro B:149	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Trp B:199 - Pro B:200	[ RasMol ]
		Trp H:199 - Pro H:200	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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	3cfd
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1fl3	CRYSTAL STRUCTURE OF BLUE FLUORESCENT ANTIBODY (19G2) IN COMPLEX WITH STILBENE HAPTEN AT 277K
1ub5	CRYSTAL STRUCTURE OF ANTIBODY 19G2 WITH HAPTEN AT 100K
1ub6	CRYSTAL STRUCTURE OF ANTIBODY 19G2 WITH SERA LIGAND
3cfb	HIGH-RESOLUTION STRUCTURE OF BLUE FLUORESCENT ANTIBODY EP2- 19G2 IN COMPLEX WITH STILBENE HAPTEN AT 100K
3cfc	HIGH-RESOLUTION STRUCTURE OF BLUE FLUORESCENT ANTIBODY EP2- 19G2
3cfe	CRYSTAL STRUCTURE OF PURPLE-FLUORESCENT ANTIBODY EP2-25C10

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (1, 8)

Pfam Domains (0, 0)

Gene Ontology (24, 37)

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