1GPO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT

Authors :   W. Schiweck, A. Skerra

Date :   27 Mar 97 (Deposition) - 01 Apr 98 (Release) - 18 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Protein Engineering, Antibody Design, Immunoglobulin Structure, Antigen-Binding Site, Canonical Conformation, Complementarity- Determining Region, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Schiweck, A. Skerra
The Rational Construction Of An Antibody Against Cystatin: Lessons From The Crystal Structure Of An Artificial Fab Fragment.
J. Mol. Biol. V. 268 934 1997
PubMed-ID: 9180382 | Reference-DOI: 10.1006/JMBI.1997.1006
(for further references see the PDB file header)

Molecule 1 - ANTIBODY M41
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK85-M41
	Expression System Strain	:	K-12 W3110
	Expression System Taxid	:	562
	Expression System Vector Type	:	BACTERIAL
	Fragment	:	FAB FRAGMENT
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ANTIBODY M41
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK85-M41
	Expression System Strain	:	K-12 W3110
	Expression System Taxid	:	562
	Expression System Vector Type	:	BACTERIAL
	Fragment	:	FAB FRAGMENT
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric Unit	:	H	I	L	M
Biological Unit 1 (1x)	:	H		L
Biological Unit 2 (1x)	:		I		M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL H:51 , GLY H:55 , THR H:70 , ARG H:71 , HOH H:705	BINDING SITE FOR RESIDUE SO4 H 650
2	AC2	SOFTWARE	VAL I:51 , GLY I:55 , THR I:70 , ARG I:71 , HOH I:527	BINDING SITE FOR RESIDUE SO4 I 651

Asymmetric Unit

No.	Residues
1	H:22	-	H:95
2	H:140	-	H:195
3	I:22	-	I:95
4	I:140	-	I:195
5	L:23	-	L:93
6	L:139	-	L:199
7	M:23	-	M:93
8	M:139	-	M:199

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Trp L:99	-	Pro L:100
3	Tyr L:145	-	Pro L:146
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Trp H:188	-	Pro H:189
7	Ser M:7	-	Pro M:8
8	Trp M:99	-	Pro M:100
9	Tyr M:145	-	Pro M:146
10	Phe I:146	-	Pro I:147
11	Glu I:148	-	Pro I:149
12	Trp I:188	-	Pro I:189

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

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:197-203 M:197-203

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:197-203 -

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:197-203

(no "Exon" information available for 1GPO)

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:214
                                                                                                                                                                                                                                                      
               SCOP domains d1gpoh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                   d1gpoh2 H:114-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1gpoH01 H:1-113 Immunoglobulins                                                                                  1gpoH02 H:114-212 Immunoglobulins                                                                  -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee.....hhh..eeeeee.....eeeeeee.....eee.hhh...eeeeee....eeeeee....hhh.eeeeeee.........eee..........eeeee..........eeeeeeeee.......eeeehhh.....eee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpo H   1 EVKLQESGPSLVKPSQTLSLTCSVTGDSITSDFWSWIRQFPGNRLEYMGFVQYSGETAYNPSLKSRISITRDTSKNQYYLDLNSVTTEDTAVYYCANWHGDYWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain I from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d1gpoi1 I:1-113 Immunoglobulin heavy chain variable domain, VH                                                   d1gpoi2 I:114-212 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1gpoI01 I:1-113 Immunoglobulins                                                                                  1gpoI02 I:114-212 Immunoglobulins                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........eeeeeeee...hhh..eeeeee.....eeeeeee.....eee.......eeeeee....eeeeee....hhh.eeeeeee.........eee..........eeeee..........eeeeeeeeeee.....eeee........eee...eee..eeeeeeeeeee........eeeeeeehhh.eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpo I   1 EVKLQESGPSLVKPSQTLSLTCSVTGDSITSDFWSWIRQFPGNRLEYMGFVQYSGETAYNPSLKSRISITRDTSKNQYYLDLNSVTTEDTAVYYCANWHGDYWGQGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain L from PDB  Type:PROTEIN  Length:216
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:216
                                                                                                                                             1                                                                                                      
                                     -         -         -         -         -         -         -         -         -         -         -   |     7        17        27        37        47        57        67        77        87        97      
           IGKC_MOUSE     - -----------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 103
               SCOP domains d1gpol1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1gpol2 L:113-216 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 1gpoL01 L:1-113 Immunoglobulins                                                                                  1gpoL02 L:114-216 Immunoglobulins                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeeee......eeeee...hhhhhh.eeeeeeeee.......eeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gpo L   1 DIELTQSPATLSVTPGNSVSISCRASQSLVNEDGNTYLFWYQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVETEDLAVYFCQQITDWPFTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 216
                                    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: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 d1gpom1 M:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1gpom2 M:113-218 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1gpoM01 M:1-113 Immunoglobulins                                                                                  1gpoM02 M:114-216 Immunoglobulins                                                                      -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...eeee..eeeee....eeeeeee............eeeeee......eeee.............eeeeee..eeeeee....hhh..eeeeee............eeeee......eeeee...hhhhh..eeeeeeeee.......-----hhh......eeeee...........eeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------eeeeee--------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpo M   1 DIELTQSPATLSVTPGNSVSISCRASQSLVNEDGNTYLFWYQQKSHESPRLLIKYASQSISGIPSRFSGSGSGTDFTLSINSVETEDLAVYFCQQITDWPFTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
                                    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(

)

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	1gpoL02	L:114-216
1b	1gpoH01	H:1-113
1c	1gpoI01	I:1-113
1d	1gpoH02	H:114-212
1e	1gpoI02	I:114-212
1f	1gpoM02	M:114-216
1g	1gpoL01	L:1-113
1h	1gpoM01	M:1-113

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

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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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Glu I:148 - Pro I:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe I:146 - Pro I:147	[ RasMol ]
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		Trp L:99 - Pro L:100	[ RasMol ]
		Trp M:99 - Pro M:100	[ RasMol ]
		Tyr L:145 - Pro L:146	[ RasMol ]
		Tyr M:145 - Pro M:146	[ RasMol ]

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	1gpo
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(no "Related Entries Specified in the PDB File" available for 1GPO)

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