2Z8W - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF AN IGNAR-AMA1 COMPLEX

Authors :   V. A. Streltsov, K. A. Henderson, A. H. Batchelor, A. M. Coley, S. D. Nutt

Date :   11 Sep 07 (Deposition) - 27 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Ama1-Vnar Complex, 14I1-M15, Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. A. Henderson, V. A. Streltsov, A. M. Coley, O. Dolezal, P. J. Hudson, A. H. Batchelor, A. Gupta, T. Bai, V. J. Murphy, R. F. Anders, M. Foley, S. D. Nuttall
Structure Of An Ignar-Ama1 Complex: Targeting A Conserved Hydrophobic Cleft Broadens Malarial Strain Recognition
Structure V. 15 1452 2007
PubMed-ID: 17997971 | Reference-DOI: 10.1016/J.STR.2007.09.011

Molecule 1 - APICAL MEMBRANE ANTIGEN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PPROEXHTB
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	DOMAIN I, II, UNP RESIDUES 104-438
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	3D7

Molecule 2 - NEW ANTIGEN RECEPTOR VARIABLE DOMAIN
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	SPOTTED WOBBEGONG
	Organism Scientific	:	ORECTOLOBUS MACULATUS
	Organism Taxid	:	168098

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2Z8W)

(no "Site" information available for 2Z8W)

Asymmetric Unit

No.	Residues
1	A:149	-	A:302
2	A:217	-	A:247
3	A:263	-	A:275
4	A:320	-	A:418
5	A:337	-	A:409
6	B:149	-	B:302
7	B:217	-	B:247
8	B:263	-	B:275
9	B:320	-	B:418
10	B:337	-	B:409
11	C:22	-	C:83
12	D:22	-	D:83

Asymmetric Unit

No.	Residues
1	Glu A:187	-	Pro A:188
2	Ser A:191	-	Pro A:192
3	Glu B:187	-	Pro B:188
4	Ser B:191	-	Pro B:192
5	Thr C:6	-	Pro C:7
6	Tyr C:94	-	Asn C:95
7	Thr D:6	-	Pro D:7
8	Tyr D:94	-	Asn D:95

(no "SAP(SNP)/Variant" information available for 2Z8W)

(no "PROSITE Motif" information available for 2Z8W)

(no "Exon" information available for 2Z8W)

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:335
 aligned with Q7KQK5_PLAF7 | Q7KQK5 from UniProtKB/TrEMBL  Length:622

    Alignment length:335
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433     
         Q7KQK5_PLAF7   104 NYMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeee...........................ee.....eehhhhhhhh....hhhhhhhhhhhhhhhhh..............eeee....eeee..........................eeee.hhhhh.eeee......hhhhhh...eeeeeeeeeee..eeee....eeee..hhhhhhhhhhhhh............hhhhhhhh.................................eeeee....eeeee.....eeeeeeeeeeee.......ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8w A 104 NYMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with Q7KQK5_PLAF7 | Q7KQK5 from UniProtKB/TrEMBL  Length:622

    Alignment length:335
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433     
         Q7KQK5_PLAF7   104 NYMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------AMA-1-2z8wB01 B:110-438                                                                                                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) ------AMA-1-2z8wB02 B:110-438                                                                                                                                                                                                                                                                                                                   Pfam domains (2)
         Sec.struct. author ......hhhhhh..hhhhhh.........eeeee..eeeee......ee..eeeee.................................eehhhhhhhh..hhhhhh.hhhhhhhhhhhh..............eeee....eeee.........................eeeee.hhhhh.eeee......hhhhhh...eeeeeeeeeee..eeee....eeee..hhhhhhhhhhhhh............hhhhhhhh.................................eeeee....eeeee.....eeeeeeeeeeee.......ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8w B 104 NYMGNPWTEYMAKYDIEEVHGSGIRVDLGEDAEVAGTQYRLPSGKCPVFGKGIIIENSNTTFLTPVATGNQYLKDGGFAFPPTEPLMSPMTLDEMRHFYKDNKYVKNLDELTLCSRHAGNMIPDNDKNSNYKYPAVYDDKDKKCHILYIAAQENNGPRYCNKDESKRNSMFCFRPAKDISFQNYTYLSKNVVDNWEKVCPRKNLQNAKFGLWVDGNCEDIPHVNEFPAIDLFECNKLVFELSASDQPKQYEQHLTDYEKIKEGFKNKNASMIKSAFLPTGAFKADRYKSHGKGYNWGNYNTETQKCEIFNVKPTCLINNSSYIATTALSHPIEVE 438
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433

Chain C from PDB  Type:PROTEIN  Length:116
 aligned with Q6X1E6_9CHON | Q6X1E6 from UniProtKB/TrEMBL  Length:113

    Alignment length:116
                                                                                                                                          113   
                                    10        20        30        40        50        60        70        80        90       100       110  |   
         Q6X1E6_9CHON     1 AWVDQTPRTATKETGESLTINCVLRDASFELKDTGWYRTKLGSTNEQSISIGGRYVETVNKGSKSFSLRISDLRVEDSGTYKCQAFYSLPLGDYNYSLLFRGEKGAGTALTVK---   -
               SCOP domains d2z8wc_ C: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee....eeeeeeee.......eeeeeeee......ee......eeeeee....eeeeee...hhhh.eeeeeeeeeeee......eeeeeeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8w C   1 AWVDQTPRTATKETGESLTINCVLRDASFELKDTGWYRTKLGSTNEQSISIGGRYVETVNKGSKSFSLRISDLRVEDSGTYKCQAFYSLLLRDYNYSLLFRGEKGAGTALTVKAAA 116
                                    10        20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:116
 aligned with Q6X1E6_9CHON | Q6X1E6 from UniProtKB/TrEMBL  Length:113

    Alignment length:116
                                                                                                                                          113   
                                    10        20        30        40        50        60        70        80        90       100       110  |   
         Q6X1E6_9CHON     1 AWVDQTPRTATKETGESLTINCVLRDASFELKDTGWYRTKLGSTNEQSISIGGRYVETVNKGSKSFSLRISDLRVEDSGTYKCQAFYSLPLGDYNYSLLFRGEKGAGTALTVK---   -
               SCOP domains d2z8wd_ D: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) V-set-2z8wD01 D:1-112                                                                                           ---- Pfam domains (1)
           Pfam domains (2) V-set-2z8wD02 D:1-112                                                                                           ---- Pfam domains (2)
         Sec.struct. author .eeeee..eeeee....eeeeeeee.......eeeeeeee.....eee......eeeeee....eeeeee...hhhh.eeeeeeeeeeeee.....eeeeeeee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2z8w D   1 AWVDQTPRTATKETGESLTINCVLRDASFELKDTGWYRTKLGSTNEQSISIGGRYVETVNKGSKSFSLRISDLRVEDSGTYKCQAFYSLLLRDYNYSLLFRGEKGAGTALTVKAAA 116
                                    10        20        30        40        50        60        70        80        90       100       110

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: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Spotted wobbegong (Orectolobus maculatus) [TaxId: 168098] (5)

1a	d2z8wc_	C:
1b	d2z8wd_	D:

(no "CATH Domain" information available for 2Z8W)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: V-set (144)

Orectolobus maculatus (spotted wobbegong) (7)

1a	V-set-2z8wD01	D:1-112
1b	V-set-2z8wD02	D:1-112

Clan: no clan defined [family: AMA-1] (6)

Family: AMA-1 (6)

Plasmodium falciparum (isolate 3D7) (4)

2a	AMA-1-2z8wB01	B:110-438
2b	AMA-1-2z8wB02	B:110-438

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q7KQK5_PLAF7 | Q7KQK5)

molecular function
	GO:0046812	host cell surface binding	Interacting selectively and non-covalently with the surface of a host cell.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0030260	entry into host cell	The invasion by an organism of a cell of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0020007	apical complex	A group of cytoskeletal structures and associated membrane-bounded organelles found at the anterior end of adult obligate intracellular protozoan parasites in the phylum Apicomplexa. The apical complex is involved in attachment to and penetration of the host cell, and in parasite proliferation.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0020009	microneme	A small, elongated secretory organelle that forms part of the apical complex, located along the main axis of an apicomplexan parasite cell within the extreme apical region and at the periphery under the inner membrane complex. Of the specialized secretory compartments identified in apicomplexans, micronemes discharge their contents first, during initial contact of the parasite's apical pole with the host cell surface. Micronemal proteins function during parasite attachment and penetration into the target cell.

Chain C,D (Q6X1E6_9CHON | Q6X1E6)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2z8w)

	Sites
(no "Sites" information available for 2z8w)

	Cis Peptide Bonds
		Glu A:187 - Pro A:188	[ RasMol ]
		Glu B:187 - Pro B:188	[ RasMol ]
		Ser A:191 - Pro A:192	[ RasMol ]
		Ser B:191 - Pro B:192	[ RasMol ]
		Thr C:6 - Pro C:7	[ RasMol ]
		Thr D:6 - Pro D:7	[ RasMol ]
		Tyr C:94 - Asn C:95	[ RasMol ]
		Tyr D:94 - Asn D:95	[ RasMol ]

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

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	2z8w
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1ver	NEW ANTIGEN RECEPTOR VARIABLE DOMAIN
1z40	APICAL MEMBRANE ANTIGEN 1 PRECURSOR, DOMAIN I AND II
2z8v	AMA1-VNAR COMPLEX, 14I-1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (12, 12)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (8, 8)

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