4YIZ - 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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ENGINEERED TGAMA1 LACKING THE DII LOOP IN COMPLEX WITH AN EIMERIA TENELLA RON2D3 PEPTIDE

Authors :   M. L. Parker, M. J. Boulanger

Date :   02 Mar 15 (Deposition) - 20 May 15 (Release) - 20 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: E,F  (1x)

Keywords :   Apicomplexa, Invasion, Moving Junction, Parasite, Protein Engineering, Pan Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Parker, M. J. Boulanger
An Extended Surface Loop On Toxoplasma Gondii Apical Membrane Antigen 1 (Ama1) Governs Ligand Binding Selectivity.
Plos One V. 10 26206 2015
PubMed-ID: 25955165 | Reference-DOI: 10.1371/JOURNAL.PONE.0126206

Molecule 1 - APICAL MEMBRANE ANTIGEN AMA1
	Chains	:	A, C, E
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Taxid	:	7111
	Expression System Vector	:	PACGP67B
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	RESIDUES 64-484
	Gene	:	TGME49_255260
	Organism Scientific	:	TOXOPLASMA GONDII ME49
	Organism Taxid	:	508771

Molecule 2 - RHOPTRY NECK PROTEIN 2, PUTATIVE
	Chains	:	B, D, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1261-1285
	Gene	:	ETH_00012760
	Organism Common	:	COCCIDIAN PARASITE
	Organism Scientific	:	EIMERIA TENELLA
	Organism Taxid	:	5802

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:					E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	A2G	1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	A2G	-1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	A2G	-1	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:239	binding site for residue SO4 A 503
2	AC2	SOFTWARE	PRO A:414 , ASN A:415 , PHE A:416	binding site for residue SO4 A 504
3	AC3	SOFTWARE	GLY C:238 , LYS C:239 , HOH C:715	binding site for residue SO4 C 502
4	AC4	SOFTWARE	LYS C:209 , ALA C:210 , HOH C:601 , HOH C:603	binding site for residue SO4 C 503
5	AC5	SOFTWARE	GLY E:238 , LYS E:239 , HOH E:747	binding site for residue SO4 E 502
6	AC6	SOFTWARE	GLU A:83 , ASN A:86 , HIS A:89 , VAL A:390	binding site for Mono-Saccharide NAG A 501 bound to ASN A 86
7	AC7	SOFTWARE	ILE A:418 , PRO A:422 , THR A:425 , PRO A:426 , PRO A:427 , HOH A:704	binding site for Mono-Saccharide A2G A 502 bound to THR A 425
8	AC8	SOFTWARE	GLU C:83 , ASN C:86 , HIS C:89 , VAL C:390	binding site for Mono-Saccharide NAG C 501 bound to ASN C 86
9	AC9	SOFTWARE	GLU E:83 , ASN E:86 , HIS E:89 , VAL E:390	binding site for Mono-Saccharide NAG E 501 bound to ASN E 86

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:1278	-	B:1288
10	C:117	-	C:286
11	C:194	-	C:226
12	C:242	-	C:255
13	C:304	-	C:393
14	C:324	-	C:384
15	C:435	-	C:459
16	C:447	-	C:471
17	C:452	-	C:479
18	D:1278	-	D:1288
19	E:117	-	E:286
20	E:194	-	E:226
21	E:242	-	E:255
22	E:304	-	E:393
23	E:324	-	E:384
24	E:435	-	E:459
25	E:447	-	E:471
26	E:452	-	E:479
27	F:1278	-	F:1288

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 C:132	-	Pro C:133
6	Asn C:153	-	Pro C:154
7	Ser C:172	-	Pro C:173
8	Glu C:247	-	Pro C:248
9	Pro E:132	-	Pro E:133
10	Asn E:153	-	Pro E:154
11	Ser E:172	-	Pro E:173
12	Glu E:247	-	Pro E:248

(no "SAP(SNP)/Variant" information available for 4YIZ)

(no "PROSITE Motif" information available for 4YIZ)

(no "Exon" information available for 4YIZ)

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:392
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhh.........eeeee..eeeee......ee..eeee.................hhhhhhhhh.....................ee.hhh.........hhhhhhhhhhhheee.............eeee....eeee...........................eeee........eeeehhhhhh...hhhhhh....eeeeeeeeee..eeee.hhh...eeee..hhhhhhhhhhhh...................eeeeee.....eeeeee.....eeeeeeeeeeee.........hhhhh..hhhhh..hhhhhh.........ee........eeeeeeee..eeeeeeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yiz A   68 SGNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPSVTPPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNEC  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

Chain B from PDB  Type:PROTEIN  Length:39
                                                                        
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh........eee...eee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                4yiz B 1259 SASDITQHLNDSGLGPAVECLENLVVGPVCPAAVVAPAV 1297
                                  1268      1278      1288

Chain C from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhh.........eeeee..eeeee......ee..eeee.................hhhhhhhhh.....................ee.hhh.........hhhhhhhhhhhheee.............eeee....eeee...........................eeee........eeeehhhhhh...hhhhhh....eeeeeeeeee..eeee.hhh...eeee..hhhhhhhhhhhh...................eeeeee.....eeeeee.....eeeeeeeeeeee.........hhhhh..hhhhh..hhhhhh.........ee........eeeeeeee..eeeeeeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yiz C   68 SGNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPSVTPPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNEC  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

Chain D from PDB  Type:PROTEIN  Length:39
                                                                        
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh........eee...eee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                4yiz D 1259 SASDITQHLNDSGLGPAVECLENLVVGPVCPAAVVAPAV 1297
                                  1268      1278      1288

Chain E from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh................eeeee..eeeee......ee..eeee.................hhhhhhhhh.....................eehhhhh........hhhhhhhhhhhheee.............eeee....eeee...........................eeee........eeeehhhhhh...hhhhhh....eeeeeeeeee..eeee.hhh...eeee..hhhhhhhhhhhh...................eeeeee.....eeeeee.....eeeeeeeeeeee.........hhhhh....hhhhhhh........ee........eeeeeeee..eeeeeeee...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yiz E   68 SGNPFQANVEMKTFMERFNLTHHHQSGIYVDLGQDKEVDGTLYREPAGLCPIWGKHIELQQPDRPPYRNNFLEDVPTEKEYKQSGNPLPGGFNLNFVTPSGQRISPFPMELLEKNSNIKASTDLGRCAEFAFKTVAMDKNNKATKYRYPFVYDSKKRLCHILYVSMQLMEGKKYCSVKGEPPDLTWYCFKPRKSVTENHHLIYGSAYVGENPDAFISKCPNQALRGYRFGVWKKGRCLDYTELTDTVIERVESKAQCWVKTFENDGVASDQPDQPHSGGVGRNYGFYYVDTTGEGKCALSDQVPDCLVSDSAAVSYTAAGSLSEETPNFIIPSNPTPETALQCTADKFPDSFGACDVQACKRQKTSCVGGQIQSTSVDCTADEQNECG  480
                                    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   ||  432       442       452       462       472        
                                                                                                                                                                                                                                                                                                         339|                                                          421|                                                     
                                                                                                                                                                                                                                                                                                          360                                                           427

Chain F from PDB  Type:PROTEIN  Length:39
                                                                        
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh........eee...eee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                4yiz F 1259 SASDITQHLNDSGLGPAVECLENLVVGPVCPAAVVAPAV 1297
                                  1268      1278      1288

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4YIZ)

(no "CATH Domain" information available for 4YIZ)

(no "Pfam Domain" information available for 4YIZ)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:153 - Pro A:154	[ RasMol ]
		Asn C:153 - Pro C:154	[ RasMol ]
		Asn E:153 - Pro E:154	[ RasMol ]
		Glu A:247 - Pro A:248	[ RasMol ]
		Glu C:247 - Pro C:248	[ RasMol ]
		Glu E:247 - Pro E:248	[ RasMol ]
		Pro A:132 - Pro A:133	[ RasMol ]
		Pro C:132 - Pro C:133	[ RasMol ]
		Pro E:132 - Pro E:133	[ RasMol ]
		Ser A:172 - Pro A:173	[ RasMol ]
		Ser C:172 - Pro C:173	[ RasMol ]
		Ser E:172 - Pro E:173	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (27, 27)

Cis Peptide Bonds (12, 12)

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