2FR4 | PD0785 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF FAB DNA-1 COMPLEXED WITH A STEM-LOOP DNA LIGAND

Authors :   J. J. Tanner, Z. Ou

Date :   18 Jan 06 (Deposition) - 09 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Antibody, Fab, Immunoglobulin, Anti-Dna, Anti-Ssdna, Autoantibody, Stem-Loop Dna, Immune System-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Ou, C. A. Bottoms, M. T. Henzl, J. J. Tanner
Impact Of Dna Hairpin Folding Energetics On Antibody-Ssdna Association.
J. Mol. Biol. V. 374 1029 2007
PubMed-ID: 18028946 | Reference-DOI: 10.1016/J.JMB.2007.09.084

*Molecule 1 - 5'-D(CPTPGPCPCPTPTPCPAPG)-3'*
	Chains	:	M, N
	Engineered	:	YES
	Other Details	:	SINGLE-STRANDED DNA OLIGONUCLEOTIDE SYNTHESIZED BY IDT
	Synthetic	:	YES

Molecule 2 - ANTIBODY LIGHT CHAIN FAB
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	ANTIGEN-BINDING FRAGMENT
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - ANTIBODY HEAVY CHAIN FAB
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	ANTIGEN-BINDING FRAGMENT
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	PG4	-1	Ligand/Ion	TETRAETHYLENE GLYCOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU H:148 , PRO H:149 , HOH H:605	BINDING SITE FOR RESIDUE PG4 H 501

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:195
5	H:22	-	H:92
6	H:140	-	H:195
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Thr L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Trp H:188	-	Pro H:189
7	Ser A:7	-	Pro A:8
8	Thr A:94	-	Pro A:95
9	Tyr A:140	-	Pro A:141
10	Phe B:146	-	Pro B:147
11	Glu B:148	-	Pro B:149
12	Trp B:188	-	Pro B:189

(no "SAP(SNP)/Variant" information available for 2FR4)

Asymmetric Unit (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 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 (, 0)

	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	0	-

(no "Exon" information available for 2FR4)

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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2fr4A01 A:1-108 Immunoglobulins                                                                             2fr4A02 A:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fr4 A    1 ELQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  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:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2fr4B01 B:1-113 Immunoglobulins                                                                                         2fr4B02 B:114-212 Immunoglobulins                                                            - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...............eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fr4 B    1 QVKLLESGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDGTKYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCVRGGYRPYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123   ||  139       149       159       169       179       189       199       209    
                                                                              52A                            82A||               100A||                        127|                                                                               
                                                                                                              82B|                100B|                         134                                                                               
                                                                                                               82C                 100C

Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2fr4H01 H:1-113 Immunoglobulins                                                                                         2fr4H02 H:114-212 Immunoglobulins                                                            - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...............eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fr4 H    1 QVKLLESGPELVKPGASVKMSCKASGYTFTSYVMHWVKQKPGQGLEWIGYINPYNDGTKYNEKFKGKATLTSDKSSSTAYMELSSLTSEDSAVYYCVRGGYRPYYAMDYWGQGTSVTVSSAKTTPPSVYPLAPNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||103       113       123  ||   139       149       159       169       179       189       199       209    
                                                                              52A                            82A||               100A||                       126|                                                                                
                                                                                                              82B|                100B|                        133                                                                                
                                                                                                               82C                 100C

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2fr4L01 L:2-108 Immunoglobulins                                                                            2fr4L02 L:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fr4 L    2 LQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain M from PDB  Type:DNA  Length:10
                                           
                2fr4 M    5 CTGCCTTCAG   14
                                    14

Chain N from PDB  Type:DNA  Length:10
                                           
                2fr4 N    5 CTGCCTTCAG   14
                                    14

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 '\|'

(no "SCOP Domain" information available for 2FR4)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

[unclassified] (54)

1a	2fr4A02	A:109-213
1b	2fr4B01	B:1-113
1c	2fr4H01	H:1-113
1d	2fr4L02	L:109-213
1e	2fr4L01	L:2-108
1f	2fr4A01	A:1-108
1g	2fr4B02	B:114-212
1h	2fr4H02	H:114-212

(no "Pfam Domain" information available for 2FR4)

Asymmetric Unit(hide GO term definitions)

Chain A (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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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Thr A:94 - Pro A:95	[ RasMol ]
		Thr L:94 - Pro L:95	[ RasMol ]
		Trp B:188 - Pro B:189	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2fr4
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	IGKC_MOUSE \| P01837
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1i8m	SAME FAB COMPLEXED WITH DT5
1xf2	SAME FAB COMPLEXED WITH DT3
1xf3	SAME FAB, UNCOMPLEXED
1xf4	SAME FAB, UNCOMPLEXED

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (1, 8)

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Gene Ontology (14, 14)

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