1E4X - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI-TGFALPHA ANTIBODY FAB-FRAGMENT

Authors :   M. Hahn, D. Winkler, R. Misselwitz, H. Wessner, K. Welfle, G. Zahn, J. Schneider-Mergener, W. Hoehne

Date :   12 Jul 00 (Deposition) - 12 Jul 01 (Release) - 08 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : H,I,L,M,P,Q
Biol. Unit 1: H,L,P  (1x)
Biol. Unit 2: I,M,Q  (1x)

Keywords :   Immune System, Complex (Antibody/Antigen), Cross-Reactivity, Protein-Peptide Recognition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hahn, D. Winkler, K. Welfle, R. Misselwitz, H. Welfle, H. Wessner, G. Zahn, C. Scholz, M. Seifert, R. Harkins, J. Schneider-Mergener, W. Hoehne
Cross-Reactive Binding Of Cyclic Peptides To An Anti-Tgf Alpha Antibody Fab Fragment: An X-Ray Structural And Thermodynamic Analysis
J. Mol. Biol. V. 314 293 2001
PubMed-ID: 11718562 | Reference-DOI: 10.1006/JMBI.2001.5135

Molecule 1 - TAB2
	Cell Line	:	MOUSE HYBRIDOMA
	Chains	:	L, M
	Fragment	:	IG KAPPA LIGHT CHAIN
	Organ	:	SPLEEN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	MURINE FAB-FRAGMENT
	Strain	:	BALB/C

Molecule 2 - TAB2
	Cell Line	:	MOUSE HYBRIDOMA
	Chains	:	H
	Fragment	:	IG KAPPA HEAVY CHAIN
	Organ	:	SPLEEN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	MURINE FAB-FRAGMENT

Molecule 3 - TAB2
	Cell Line	:	MOUSE HYBRIDOMA
	Chains	:	I
	Fragment	:	IG KAPPA HEAVY CHAIN
	Organ	:	SPLEEN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	MURINE FAB-FRAGMENT

Molecule 4 - CYCLIC PEPTIDE
	Chains	:	P, Q
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1E4X)

(no "Site" information available for 1E4X)

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	H:125	-	L:214
3	H:137	-	H:192
4	I:22	-	I:92
5	I:125	-	M:214
6	I:137	-	I:192
7	L:23	-	L:88
8	L:134	-	L:194
9	M:23	-	M:88
10	M:134	-	M:194

Asymmetric Unit

No.	Residues
1	Phe H:143	-	Pro H:144
2	Glu H:145	-	Pro H:146
3	Trp H:185	-	Pro H:186
4	Phe I:143	-	Pro I:144
5	Glu I:145	-	Pro I:146
6	Trp I:185	-	Pro I:186
7	Thr L:7	-	Pro L:8
8	Leu L:94	-	Pro L:95
9	Tyr L:140	-	Pro L:141
10	Thr M:7	-	Pro M:8
11	Leu M:94	-	Pro M:95
12	Tyr M:140	-	Pro M:141

(no "SAP(SNP)/Variant" information available for 1E4X)

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	L:192-198 M: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	L: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	- M:192-198

(no "Exon" information available for 1E4X)

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:216
                                                                                                                                                                                                                                                        
               SCOP domains d1e4xh1 H:1-110 Immunoglobulin heavy chain variable domain, VH                                                    d1e4xh2 H:111-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1e4xH01 H:1-110 Immunoglobulins                                                                                   1e4xH02 H:111-209 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeee.......eeeeeee.....eeeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e4x H   1 QVQLQQPGAELVKPGASVKLSCKASGFTFTNYWMHWVKQRPGQGLEWIGEILPSNGRTNYNEKFKTKATLTVDKSSNTAYMQLSSLTSEDSAVYYCARSPSDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRVP 212
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206      
                                                                              52A                            82A||                                                                                                                                  
                                                                                                              82B|                                                                                                                                  
                                                                                                               82C

Chain I from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1e4xi1 I:1-110 Immunoglobulin heavy chain variable domain, VH                                                    d1e4xi2 I:111-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1e4xI01 I:1-110 Immunoglobulins                                                                                   1e4xI02 I:111-209 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4x I   1 QVQLQQPGAELVKPGPSVKLSCKASGFTFTNYWMHWVKQRPGQGLEWIGEILPSNGRTNYNEKFKTKATLTVDKSSNTAYMQLSSLTSEDSAVYYCARSPSDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRVPI 213
                                    10        20        30        40        50  |     59        69        79   |||  86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                                              52A                            82A||                                                                                                                                   
                                                                                                              82B|                                                                                                                                   
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:214
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:214
                                                                                                                                        1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102    
           IGKC_MOUSE     - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 106
               SCOP domains d1e4xl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1e4xl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1e4xL01 L:1-108 Immunoglobulins                                                                             1e4xL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeee.......eeeeee........eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4x L   1 DIQMTQTPSSLSASLGDRVTISCRASQDISHYLNWFQQKPDGTVKLLIYYTSTLHSGVPSRFSGSGSGTDYSLTISNLEEEDIAFYFCQQGGALPFTFGSGTKLAIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLDSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain M from PDB  Type:PROTEIN  Length:214
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:214
                                                                                                                                        1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102    
           IGKC_MOUSE     - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 106
               SCOP domains d1e4xm1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1e4xm2 M:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1e4xM01 M:1-107 Immunoglobulins                                                                            1e4xM02 M:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..hhhhhhh.eeeeeeeee.......eeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e4x M   1 DIQMTQTPSSLSASLGDRVTISCRASQDISHYLNWFQQKPDGTVKLLIYYTSTLHSGVPSRFSGSGSGTDYSLTISNLEEEDIAFYFCQQGGALPFTFGSGTKLAIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLDSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain P from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1e4x P   1 VVSHFND   7

Chain Q from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1e4x Q   1 VVSHFND   7

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	1e4xM02	M:108-211
1b	1e4xH02	H:111-209
1c	1e4xI02	I:111-209
1d	1e4xL02	L:109-211
1e	1e4xH01	H:1-110
1f	1e4xI01	I:1-110
1g	1e4xM01	M:1-107
1h	1e4xL01	L:1-108

(no "Pfam Domain" information available for 1E4X)

Asymmetric Unit(hide GO term definitions)

Chain L,M (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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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1e4x)

	Sites
(no "Sites" information available for 1e4x)

	Cis Peptide Bonds
		Glu H:145 - Pro H:146	[ RasMol ]
		Glu I:145 - Pro I:146	[ RasMol ]
		Leu L:94 - Pro L:95	[ RasMol ]
		Leu M:94 - Pro M:95	[ RasMol ]
		Phe H:143 - Pro H:144	[ RasMol ]
		Phe I:143 - Pro I:144	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Thr M:7 - Pro M:8	[ RasMol ]
		Trp H:185 - Pro H:186	[ RasMol ]
		Trp I:185 - Pro I:186	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr M:140 - Pro M:141	[ RasMol ]

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	1e4x
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1e4w	CROSSREACTIVE BINDING OF A CIRCULARIZED PEPTIDE TO AN ANTI-TGFALPHA ANTIBODY FAB-FRAGMENT
1fbi	FAB FRAGMENT OF THE MONOCLONAL ANTIBODY F9.13.7 (IGG1) COMPLEXED WITH LYSOZYME

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (10, 10)

Cis Peptide Bonds (12, 12)

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