3C5S - JenaLib

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Title :   CRYSTAL STRUCTURE OF MONOCLONAL FAB F22-4 SPECIFIC FOR SHIGELLA FLEXNERI 2A O-AG

Authors :   F. A. Saul, B. Vulliez-Le-Normand, G. A. Bentley

Date :   01 Feb 08 (Deposition) - 01 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Antibody, O-Antigen, Lps, Shigella Flexneri, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Vulliez-Le Normand, F. A. Saul, A. Phalipon, F. Belot, C. Guerreiro, L. A. Mulard, G. A. Bentley
Structures Of Synthetic O-Antigen Fragments From Serotype 2A Shigella Flexneri In Complex With A Protective Monoclonal Antibody
Proc. Natl. Acad. Sci. Usa V. 105 9976 2008
PubMed-ID: 18621718 | Reference-DOI: 10.1073/PNAS.0801711105
(for further references see the PDB file header)

Molecule 1 - FAB F22-4 LIGHT CHAIN
	Chains	:	A, C
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

Molecule 2 - FAB F22-4 HEAVY CHAIN
	Chains	:	B, D
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Strain	:	BALB/C

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3C5S)

(no "Site" information available for 3C5S)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:142	-	B:197
5	C:23	-	C:88
6	C:134	-	C:194
7	D:22	-	D:92
8	D:142	-	D:197

Asymmetric Unit

No.	Residues
1	Leu A:94	-	Pro A:95
2	Tyr A:140	-	Pro A:141
3	Pro B:95	-	Met B:96
4	Phe B:148	-	Pro B:149
5	Glu B:150	-	Pro B:151
6	Trp B:190	-	Pro B:191
7	Leu C:94	-	Pro C:95
8	Tyr C:140	-	Pro C:141
9	Pro D:95	-	Met D:96
10	Phe D:148	-	Pro D:149
11	Glu D:150	-	Pro D:151
12	Trp D:190	-	Pro D:191

(no "SAP(SNP)/Variant" information available for 3C5S)

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 C: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	- C:192-198

(no "Exon" information available for 3C5S)

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:218
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:218
                                                                                                                                             1                                                                                                        
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97        
           IGKC_MOUSE     - -----------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 105
               SCOP domains d3c5sa1 A:1-107 automated matches                                                                               d3c5sa2 A:108-213 automated matches                                                                        SCOP domains
               CATH domains 3c5sA01 A:1-108 Immunoglobulins                                                                                  3c5sA02 A:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee....eeeeeee............eeeeee.....eeeeee...ee.......eeeee...eeeeee...hhhhheeeeeee...........eee.ee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5s A   1 DIVMTQAAFSNPVTLGTSASISCRSSKSLLHSDGITYLYWYLQKPGQSPHLLIYHLSNLASGVPDRFSSSGSGTDFTLRISRVEAEDVGIYYCAHNVELPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3c5sB01 B:1-113 Immunoglobulins                                                                          3c5sB02 B:114-215 Immunoglobulins                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee.....eeeeeee...eeeeeeee..ee.hhhh..eeeeee....eeeeee...hhhhheeeeeee...ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c5s B   1 EVKVEESGGGLVQPGGSMKISCVVSGSNYWMSWVRQSPEKGLEWVAEIRTYYAESVKGKFTISRDDSKSRLYLQMNNLRTEDTGIYYCFLPMDYWGQGTSVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 215
                                    10        20     || 33        43        57        67        77     |||84        94 ||    108       118       137       147       157       167       177       187       197       207        
                                                    26|                    52|                       82A||            96|                      126|                                                                               
                                                     30                     57                        82B|            101                       136                                                                               
                                                                                                       82C

Chain C from PDB  Type:PROTEIN  Length:217
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:217
                                                                                                                                             1                                                                                                       
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97       
           IGKC_MOUSE     - -----------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 104
               SCOP domains d3c5sc1 C:1-107 automated matches                                                                               d3c5sc2 C:108-212 automated matches                                                                       SCOP domains
               CATH domains 3c5sC01 C:1-108 Immunoglobulins                                                                                  3c5sC02 C:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......ee....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee...........ee..ee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5s C   1 DIVMTQAAFSNPVTLGTSASISCRSSKSLLHSDGITYLYWYLQKPGQSPHLLIYHLSNLASGVPDRFSSSGSGTDFTLRISRVEAEDVGIYYCAHNVELPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                     27A||||                                                                                                                                                                                         
                                                      27B|||                                                                                                                                                                                         
                                                       27C||                                                                                                                                                                                         
                                                        27D|                                                                                                                                                                                         
                                                         27E

Chain D from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c5sD01 D:1-113 Immunoglobulins                                                                                    3c5sD02 D:114-215 Immunoglobulins                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeee...ee...eeeee........eeeee...eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5s D   1 EVKVEESGGGLVQPGGSMKISCVVSGLTFSNYWMSWVRQSPEKGLEWVAEIRLKSDNYATYYAESVKGKFTISRDDSKSRLYLQMNNLRTEDTGIYYCFLPMDYWGQGTSVTVSSAKTTPPSVYPLAPSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 215
                                    10        20        30        40        50  |||   57        67        77     |||84        94 ||    108       118       137       147       157       167       177       187       197       207        
                                                                              52A||                            82A||            96|                      126|                                                                               
                                                                               52B|                             82B|            101                       136                                                                               
                                                                                52C                              82C

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	d3c5sa1	A:1-107
1b	d3c5sc1	C:1-107

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

Protein domain: automated matches (652)

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

2a	d3c5sa2	A:108-213
2b	d3c5sc2	C:108-212

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Mouse (Mus musculus) (152)

1a	3c5sA02	A:109-213
1b	3c5sB02	B:114-215
1c	3c5sD02	D:114-215
1d	3c5sA01	A:1-108
1e	3c5sC01	C:1-108
1f	3c5sB01	B:1-113
1g	3c5sD01	D:1-113
1h	3c5sC02	C:109-212

(no "Pfam Domain" information available for 3C5S)

Asymmetric Unit(hide GO term definitions)

Chain A,C (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 3c5s)

	Sites
(no "Sites" information available for 3c5s)

	Cis Peptide Bonds
		Glu B:150 - Pro B:151	[ RasMol ]
		Glu D:150 - Pro D:151	[ RasMol ]
		Leu A:94 - Pro A:95	[ RasMol ]
		Leu C:94 - Pro C:95	[ RasMol ]
		Phe B:148 - Pro B:149	[ RasMol ]
		Phe D:148 - Pro D:149	[ RasMol ]
		Pro B:95 - Met B:96	[ RasMol ]
		Pro D:95 - Met D:96	[ RasMol ]
		Trp B:190 - Pro B:191	[ RasMol ]
		Trp D:190 - Pro D:191	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr C:140 - Pro C:141	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	3c5s
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3bz4	FAB F22-4 IN COMPLEX WITH A SHIGELLA FLEXNERI 2A O-AG DECASACCHARIDE
3c6s	FAB F22-4 IN COMPLEX WITH A SHIGELLA FLEXNERI 2A O-AG PENTADECASACCHARIDE

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

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