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Title :   COMPLEX OF THE NEISSERIAL PORA P1.4 EPITOPE PEPTIDE AND TWO FAB-FRAGMENTS (ANTIBODY MN20B9.34)

Authors :   C. J. Oomen, P. Hoogerhout, B. Kuipers, G. Vidarsson, L. Van Alphen, P

Date :   11 May 05 (Deposition) - 27 Jul 05 (Release) - 16 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : H,L,P,X,Y

Keywords :   Immune System, Fab Fragment, Anti-Pora Antibody, P1. 4 Antibody, Antigen, Porin, Transmembrane, Antibody/Antigen Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Oomen, P. Hoogerhout, B. Kuipers, G. Vidarsson, L. Van Alphen, P. Gros
Crystal Structure Of An Anti-Meningococcal Subtype P1. 4 Pora Antibody Provides Basis For Peptide- Vaccine Design.
J. Mol. Biol. V. 351 1070 2005
PubMed-ID: 16038932 | Reference-DOI: 10.1016/J.JMB.2005.06.061

Molecule 1 - MN20B9.34 ANTI-P1.4 ANTIBODY, FAB HEAVY CHAIN
	Cell Line	:	MN20B9.34 MURINE HYBRIDOMA
	Chains	:	H, Y
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - MN20B9.34 ANTI-P1.4 ANTIBODY, FAB LIGHT CHAIN
	Cell Line	:	MN20B9.34 MURINE HYBRIDOMA
	Chains	:	L, X
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - CLASS 1 OUTER MEMBRANE PROTEIN VARIABLE REGION 2
	Chains	:	P
	Fragment	:	EXTRACELLULAR LOOP 4 OF PORA SUBTYPE P1.4, RESIDUES 16-26
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	487
	Other Details	:	N-TERMINUS ACETYLATED, C-TERMINUS AMIDATED
	Strain	:	SUBTYPE P1.4
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric/Biological Unit	:	H	L	P	X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	NH2	1	Mod. Amino Acid	AMINO GROUP
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR X:182 , ASP X:184 , ARG X:188	BINDING SITE FOR RESIDUE SO4 X1215
2	AC2	SOFTWARE	ALA Y:1 , VAL Y:2 , TYR Y:102	BINDING SITE FOR RESIDUE SO4 Y1216
3	AC3	SOFTWARE	ASP X:167 , HOH X:2055 , HIS Y:164	BINDING SITE FOR RESIDUE ACY X1216

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:128	-	L:214
3	H:140	-	H:195
4	L:23	-	L:88
5	L:134	-	L:194
6	X:23	-	X:88
7	X:134	-	X:194
8	X:214	-	Y:128
9	Y:22	-	Y:92
10	Y:140	-	Y:195

Asymmetric/Biological Unit

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

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

(no "PROSITE Motif" information available for 2BRR)

(no "Exon" information available for 2BRR)

Asymmetric/Biological 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:224
                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------d2brrh1 H:115-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     - SCOP domains
               CATH domains 2brrH01 H:2-113 Immunoglobulins                                                                                           2brrH02 H:114-215 Immunoglobulins                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeeeeee...eeeee........eeeee.hhhhh....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2brr H    2 VQLEQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKERFAFSLETSASAAYLQINNLKNEDTATYFCARDYYGSTYPYYAMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGG  215
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||||101       111       121       131       141       151       161       171       181       191       201       211    
                                                                             52A                            82A||               100A|||||                                                                                                                   
                                                                                                             82B|                100B||||                                                                                                                   
                                                                                                              82C                 100C|||                                                                                                                   
                                                                                                                                   100D||                                                                                                                   
                                                                                                                                    100E|                                                                                                                   
                                                                                                                                     100F

Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d2brrl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d2brrl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2brrL01 L:1-108 Immunoglobulins                                                                              2brrL02 L:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....hhh.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2brr L    1 ENVLTQSPAIMSASPGEKVTMTCRASSSVSSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYSGYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209     
                                                     27A

Chain P from PDB  Type:PROTEIN  Length:10
 aligned with Q51183_NEIME | Q51183 from UniProtKB/TrEMBL  Length:58

    Alignment length:10
                                    27
        Q51183_NEIME     18 VVNNKVATHV   27
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .ee..ee... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                2brr P    3 VVNNKVATHx   12
                                    12
                                    12-NH2

Chain X from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2brrx1 X:2-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d2brrx2 X:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 2brrX01 X:2-108 Immunoglobulins                                                                             2brrX02 X:109-211 Immunoglobulins                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeeeeeeehhh.eeeeee......eeeee...ee.......eeeeeeeeeeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2brr X    2 NVLTQSPAIMSASPGEKVTMTCRASSSVSSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQYSGYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    11        21      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
                                                    27A

Chain Y from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------d2brry1 Y:115-214 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     - SCOP domains
               CATH domains 2brrY01 Y:1-113 Immunoglobulins                                                                                            2brrY02 Y:114-215 Immunoglobulins                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeeee....eeeeeeee...eeeee........eeeee.hhhhh....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2brr Y    1 AVQLEQSGPELKKPGETVKISCKASGYTFTNYGMNWVKQAPGKGLKWMGWINTYTGEPTYADDFKERFAFSLETSASAAYLQINNLKNEDTATYFCARDYYGSTYPYYAMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGG  215
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       130       140       150       160       170       180       190       200       210     
                                                                              52A                            82A||               100A|||||                                                                                                                   
                                                                                                              82B|                100B||||                                                                                                                   
                                                                                                               82C                 100C|||                                                                                                                   
                                                                                                                                    100D||                                                                                                                   
                                                                                                                                     100E|                                                                                                                   
                                                                                                                                      100F

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/Biological 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	2brrL02	L:109-211
1b	2brrX01	X:2-108
1c	2brrL01	L:1-108
1d	2brrH02	H:114-215
1e	2brrY02	Y:114-215
1f	2brrH01	H:2-113
1g	2brrY01	Y:1-113
1h	2brrX02	X:109-211

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain P (Q51183_NEIME | Q51183)

molecular function
	GO:0015288	porin activity	Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Glu Y:148 - Pro Y:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe Y:146 - Pro Y:147	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser X:7 - Pro X:8	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Trp Y:188 - Pro Y:189	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr L:94 - Pro L:95	[ RasMol ]
		Tyr X:140 - Pro X:141	[ RasMol ]
		Tyr X:94 - Pro X:95	[ RasMol ]

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	2brr
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

SS Bonds (10, 10)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

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