2Y8T - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CO-STRUCTURE OF AMA1 WITH A SURFACE EXPOSED REGION OF RON2 FROM TOXOPLASMA GONDII

Authors :   M. L. Tonkin, M. Roques, M. H. Lamarque, M. Pugniere, D. Douguet, J. Craw M. Lebrun, M. J. Boulanger

Date :   10 Feb 11 (Deposition) - 03 Aug 11 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Membrane Protein, Moving Junction, Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Tonkin, M. Roques, M. H. Lamarque, M. Pugniere, D. Douguet, J. Crawford, M. Lebrun, M. J. Boulanger
Host Cell Invasion By Apicomplexan Parasites: Insights From The Co-Structure Of Ama1 With A Ron2 Peptide
Science V. 333 463 2011
PubMed-ID: 21778402 | Reference-DOI: 10.1126/SCIENCE.1204988

Molecule 1 - APICAL MEMBRANE ANTIGEN, PUTATIVE
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH-FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	DOMAINS I/II/III, RESIDUES 64-484
	Organism Scientific	:	TOXOPLASMA GONDII
	Organism Taxid	:	5811
	Synonym	:	AMA1, APICAL MEMBRANE ANTIGEN 1

Molecule 2 - RHOPTRY NECK PROTEIN 2
	Chains	:	B, E
	Fragment	:	RESIDUES 235-271
	Organism Scientific	:	TOXOPLASMA GONDII
	Organism Taxid	:	5811
	Synonym	:	RON2
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	9AT	1	Mod. Amino Acid	(2S,3R)-2-AMINO-3-HYDROXY-BUTANAMIDE
2	BO3	2	Ligand/Ion	BORIC ACID
3	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	9AT	1	Mod. Amino Acid	(2S,3R)-2-AMINO-3-HYDROXY-BUTANAMIDE
2	BO3	-1	Ligand/Ion	BORIC ACID
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	9AT	-1	Mod. Amino Acid	(2S,3R)-2-AMINO-3-HYDROXY-BUTANAMIDE
2	BO3	2	Ligand/Ion	BORIC ACID
3	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:83 , ASN A:86 , THR A:88 , HIS A:89 , VAL A:390 , HOH A:2315 , HOH A:2317 , HOH A:2318	BINDING SITE FOR RESIDUE NAG A1480
2	AC2	SOFTWARE	ASN D:86 , THR D:88 , HIS D:89 , HOH D:2009 , HOH D:2240	BINDING SITE FOR RESIDUE NAG D1474
3	AC3	SOFTWARE	HOH D:2241	BINDING SITE FOR RESIDUE BO3 D1475
4	AC4	SOFTWARE	ASP D:102 , HOH D:2242	BINDING SITE FOR RESIDUE BO3 D1476

Asymmetric Unit

No.	Residues
1	A:117	-	A:286
2	A:194	-	A:226
3	A:242	-	A:255
4	A:304	-	A:393
5	A:324	-	A:384
6	A:435	-	A:459
7	A:447	-	A:471
8	A:452	-	A:479
9	B:1313	-	B:1323
10	D:117	-	D:286
11	D:194	-	D:226
12	D:242	-	D:255
13	D:304	-	D:393
14	D:324	-	D:384
15	D:435	-	D:459
16	D:447	-	D:471
17	E:1313	-	E:1323

Asymmetric Unit

No.	Residues
1	Pro A:132	-	Pro A:133
2	Asn A:153	-	Pro A:154
3	Ser A:172	-	Pro A:173
4	Glu A:247	-	Pro A:248
5	Pro D:132	-	Pro D:133
6	Asn D:153	-	Pro D:154
7	Ser D:172	-	Pro D:173
8	Glu D:247	-	Pro D:248
9	Trp D:354	-	Pro D:355

(no "SAP(SNP)/Variant" information available for 2Y8T)

(no "PROSITE Motif" information available for 2Y8T)

(no "Exon" information available for 2Y8T)

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:388
 aligned with AMA1_TOXGV | B6KAM0 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:412
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477  
          AMA1_TOXGV     68 SGNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPHTYPLTSQASWNDWWPLHQSDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPSVTPPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNEC  479
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh................eeeee..eeeee......ee..eeee.................hhhhhhhhh.....................eehhhhhh.......hhhhhhhhhhhheee.............eeee....eeee.............ee.........ee.eeee........eeeehhhhhh...hhhhhh....eeeeeeeeee..eeee.hhh...eeee..hhhhhhhhhhhh........--------------------...........eeeeee.....eeeeee.....eeeeeeeeeeee.........hhhhh...----..hhhhhh..hhhhh..ee........eeeeeeee..eeeeeeee.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y8t A   68 SGNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQP--------------------DQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSN----PPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNEC  479
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337 |       -         -  |    367       377       387       397       407       417   |   427       437       447       457       467       477  
                                                                                                                                                                                                                                                                                                         339                  360                                                          421  426

Chain B from PDB  Type:PROTEIN  Length:37
 aligned with RON2_TOXGM | B6KV60 from UniProtKB/Swiss-Prot  Length:1479

    Alignment length:37
                                  1306      1316      1326       
          RON2_TOXGM   1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKATT 1333
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.......eeee...eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                2y8t B 1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKATt 1333
                                  1306      1316      1326      |
                                                             1333-9AT

Chain D from PDB  Type:PROTEIN  Length:395
 aligned with AMA1_TOXGV | B6KAM0 from UniProtKB/Swiss-Prot  Length:569

    Alignment length:405
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468     
          AMA1_TOXGV     69 GNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPHTYPLTSQASWNDWWPLHQSDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPSVTPPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTA  473
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh................eeeee..eeeee......ee..eeee.................hhhhhhhhh.....................eehhhhhh.......hhhhhhhhhhhheee.............eeee....eeee.............ee.........ee.eeee........eeeehhhhhh..hhhhhhh....eeeeeeeeee..eeee.hhh...eeee..hhhhhhhhhhhh................---....................eeeeee.....eeeeee.....eeeeeeeeeeee.........hhhhh...-------hhhhh..hhhhh..ee........eeeeeeee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y8t D   69 GNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPHTYPLTSQ---NDWWPLHQSDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSN-------PETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTA  473
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338        |-  |    358       368       378       388       398       408       418  |      -|      438       448       458       468     
                                                                                                                                                                                                                                                                                                                347 351                                                                   421     429

Chain E from PDB  Type:PROTEIN  Length:36
 aligned with RON2_TOXGM | B6KV60 from UniProtKB/Swiss-Prot  Length:1479

    Alignment length:36
                                  1306      1316      1326      
          RON2_TOXGM   1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKAT 1332
               SCOP domains ------------------------------------ SCOP domains
               CATH domains ------------------------------------ CATH domains
               Pfam domains ------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.......eeee...eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                2y8t E 1297 DIVQHMEDIGGAPPVSCVTNEILGVTCAPQAIAKAT 1332
                                  1306      1316      1326

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 '\|'

(no "SCOP Domain" information available for 2Y8T)

(no "CATH Domain" information available for 2Y8T)

(no "Pfam Domain" information available for 2Y8T)

Asymmetric Unit(hide GO term definitions)

Chain A,D (AMA1_TOXGV | B6KAM0)

biological process
	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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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: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.

Chain B,E (RON2_TOXGM | B6KV60)


GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		9AT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BO3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Asn A:153 - Pro A:154	[ RasMol ]
		Asn D:153 - Pro D:154	[ RasMol ]
		Glu A:247 - Pro A:248	[ RasMol ]
		Glu D:247 - Pro D:248	[ RasMol ]
		Pro A:132 - Pro A:133	[ RasMol ]
		Pro D:132 - Pro D:133	[ RasMol ]
		Ser A:172 - Pro A:173	[ RasMol ]
		Ser D:172 - Pro D:173	[ RasMol ]
		Trp D:354 - Pro D:355	[ RasMol ]

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

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	2y8t
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	AMA1_TOXGV \| B6KAM0
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	RON2_TOXGM \| B6KV60
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	AMA1_TOXGV \| B6KAM0
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UniProtKB/Swiss-Prot
	AMA1_TOXGV \| B6KAM0	:	2x2z 2y8r 2y8s
	RON2_TOXGM \| B6KV60	:	2y8s

2y8r	CRYSTAL STRUCTURE OF APO AMA1 MUTANT (TYR230ALA) FROM TOXOPLASMA GONDII
2y8s	CO-STRUCTURE OF AN AMA1 MUTANT (Y230A) WITH A SURFACE EXPOSED REGION OF RON2 FROM TOXOPLASMA GONDII

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (17, 17)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (8, 11)

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