1YNT: Monomeric form of T. gondii SAG1 surface antigen

Structure of the monomeric form of T. gondii SAG1 surface antigen bound to a human Fab. Determined by X-ray diffraction at 3.1 Å resolution. Released 27 Dec 2005.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Mus musculus, Finegoldia magna, Toxoplasma gondii
Chains: 7
Atoms: 10,802
Mol. weight: 154.55 kDa
Ligands: CD
Released: 27 Dec 2005

Explore 1YNT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YNT contains 32 α-helices and 158 β-strands across 7 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	8-10	3	2
β-strand	13	1	3
β-strand	19-24	6	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	85-90	6	2
β-strand	97-98	2	2
β-strand	102-103	2	2
β-strand	106	1	3
β-strand	111	1	4
β-strand	114-117	4	5
α-helix	122-125	4
β-strand	129-130	2	6
β-strand	133-139	7	5
β-strand	140	1	4
β-strand	145-146	2	7
β-strand	149-150	2	7
β-strand	153-154	2	7
β-strand	159-163	5	5
α-helix	164-166	3
β-strand	173-179	7	5
β-strand	181-182	2	6
α-helix	183-186	4
β-strand	191-197	7	7
α-helix	204	1
β-strand	205-210	6	7

Chain B: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	503-505	3	8
β-strand	510-512	3	9
β-strand	518-520	3	8
β-strand	523-525	3	8
β-strand	533-539	7	9
β-strand	546-552	7	9
β-strand	558-559	2	9
α-helix	562-564	3
β-strand	565	1	10
β-strand	568	1	10
β-strand	570-573	4	8
α-helix	574-576	3
β-strand	578-583	6	8
β-strand	592-599	8	9
β-strand	607-608	2	9
β-strand	612-616	5	9
β-strand	622	1	11
α-helix	623-624	2
β-strand	625-629	5	12
α-helix	630-632	3
β-strand	640-650	11	12
β-strand	651	1	11
β-strand	656-659	4	13
β-strand	664	1	13
β-strand	669-676	8	12
β-strand	679-689	11	12
β-strand	699-704	6	13
α-helix	705-707	3
β-strand	709-714	6	13

Chain C: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	1005	1	14
β-strand	1008	1	15
β-strand	1010	1	16
β-strand	1013	1	17
β-strand	1019-1024	6	14
β-strand	1033-1038	6	16
β-strand	1045-1049	5	16
β-strand	1053-1054	2	16
β-strand	1062-1067	6	14
β-strand	1070-1075	6	14
α-helix	1080-1082	3
β-strand	1085-1090	6	16
β-strand	1097-1098	2	16
β-strand	1102-1103	2	16
β-strand	1106	1	17
β-strand	1111	1	18
β-strand	1114-1117	4	19
α-helix	1122-1125	4
β-strand	1129-1130	2	20
β-strand	1133-1139	7	19
β-strand	1140	1	18
β-strand	1145-1146	2	21
β-strand	1149-1150	2	21
β-strand	1153-1154	2	21
β-strand	1159-1163	5	19
α-helix	1164-1166	3
β-strand	1173-1179	7	19
β-strand	1181-1182	2	20
α-helix	1183-1186	4
β-strand	1191-1197	7	21
α-helix	1204	1
β-strand	1205-1210	6	21

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	1503-1505	3	22
β-strand	1510-1512	3	23
β-strand	1518-1520	3	22
β-strand	1523-1525	3	22
β-strand	1533-1539	7	23
β-strand	1546-1551	6	23
β-strand	1558-1559	2	23
α-helix	1562-1564	3
β-strand	1565	1	24
β-strand	1568	1	24
β-strand	1570-1573	4	22
α-helix	1574-1576	3
β-strand	1578-1583	6	22
β-strand	1592-1599	8	23
β-strand	1607-1608	2	23
β-strand	1612-1616	5	23
β-strand	1622	1	25
α-helix	1623-1624	2
β-strand	1625-1629	5	26
α-helix	1630-1632	3
β-strand	1640-1650	11	26
β-strand	1651	1	25
β-strand	1656-1659	4	27
α-helix	1660-1662	3
β-strand	1664	1	27
β-strand	1669-1676	8	26
β-strand	1679-1689	11	26
β-strand	1699-1704	6	27
α-helix	1705-1707	3
β-strand	1709-1714	6	27

Chain E: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	821-828	8	2
β-strand	834-841	8	2
α-helix	845-861	17
β-strand	864	1	15
β-strand	865-868	4	2
β-strand	875-878	4	2

Chain F: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2005-2006	2	28
β-strand	2009-2011	3	28
β-strand	2019-2023	5	29
β-strand	2024	1	30
β-strand	2027	1	30
β-strand	2031-2033	3	28
β-strand	2039-2040	2	31
α-helix	2043-2046	4
β-strand	2052	1	32
β-strand	2055	1	29
β-strand	2068	1	32
α-helix	2069-2071	3
α-helix	2078-2080	3
β-strand	2081-2083	3	28
β-strand	2093-2095	3	28
α-helix	2099-2101	3
β-strand	2107-2110	4	29
β-strand	2113-2115	3	31
β-strand	2117-2122	6	31
β-strand	2124-2128	5	29
β-strand	2134-2135	2	33
β-strand	2139-2141	3	33
β-strand	2148-2154	7	34
β-strand	2162-2166	5	33
β-strand	2171-2174	4	34
β-strand	2182	1	34
α-helix	2187-2189	3
β-strand	2192	1	34
β-strand	2218-2220	3	33
β-strand	2231-2239	9	34
β-strand	2245-2253	9	34

Chain G: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3005-3006	2	35
β-strand	3009-3011	3	35
β-strand	3019-3023	5	36
β-strand	3024	1	37
β-strand	3027	1	37
β-strand	3031-3033	3	35
β-strand	3039-3040	2	38
α-helix	3043-3046	4
β-strand	3052	1	39
β-strand	3055	1	36
β-strand	3068	1	39
α-helix	3069-3071	3
α-helix	3078-3080	3
β-strand	3081-3083	3	35
β-strand	3093-3095	3	35
α-helix	3099-3101	3
β-strand	3107-3110	4	36
β-strand	3113-3115	3	38
β-strand	3117-3122	6	38
β-strand	3124-3128	5	36
β-strand	3134-3135	2	40
β-strand	3139-3141	3	40
β-strand	3148-3154	7	41
β-strand	3162-3166	5	40
β-strand	3171-3174	4	41
β-strand	3182	1	41
α-helix	3187-3189	3
β-strand	3192	1	41
β-strand	3218-3220	3	40
β-strand	3231-3239	9	41
β-strand	3245-3253	9	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
4F11E12 Fab variable light chain region	A, C	protein	213	Mus musculus
4F11E12 Fab variable heavy chain region	B, D	protein	218	Mus musculus
protein L	E	protein	61	Finegoldia magna	Q51918 (AlphaFold model)
Major surface antigen p30	F, G	protein	254	Toxoplasma gondii	P13664 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1YNT_1 4F11E12 Fab variable light chain region (chains A, C)
DIQVTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
RFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 2 (B, D), FASTA

>1YNT_2 4F11E12 Fab variable heavy chain region (chains B, D)
QVQLQQSGAELVRPGVSVKISCKGSGYTFTDYGMHWVKQSHAKSLEWIGIISTYSGDASY
NQKFKGKATMTVDKSSSTAYMELARLTSEDSAIYYCARSSTWYYFDYWGQGTTLTVSSAK
TTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLY
TLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Sequence of entity 3 (E), FASTA

>1YNT_3 protein L (chains E)
EVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYADLLAKVNGEYTADLEDGGNHMNIKF
A

Sequence of entity 4 (F, G), FASTA

>1YNT_4 Major surface antigen p30 (chains F, G)
PPLVANQVVTCPDKKSTAAVILTPTENHFTLKCPKTALTEPPTLAYSPNRQICPAGTTSS
CTSKAVTLSSLIPEAEDSWWTGDSASLDTAGIKLTVPIEKFPVTTQTFVVGCIKGDDAQS
CMVTVTVQARASSVVNNVARCSYGADSTLGPVKLSAEGPTTMTLVCGKDGVKVPQDNNQY
CSGTTLTGCNEKSFKDILPKLTENPWQGNASSDKGATLTIKKEAFPAESKSVIIGCTGGS
PEKHHCTVKLEFAG

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	2

Primary citation

Crystal structure of the complex between the monomeric form of Toxoplasma gondii surface antigen 1 (SAG1) and a monoclonal antibody that mimics the human immune response. Graille, M., Stura, E.A., Bossus, M. et al. J Mol Biol (2005) 354:447-458. DOI 10.1016/j.jmb.2005.09.028 · PubMed

Other PDB entries of the same protein (UniProt Q51918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5U6A 1.74 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-PEG3-meditope
5U3D 1.77 Å, Structure of meditope enabled trastuzumab I83E variant
5U5F 1.81 Å, Meditope enabled trastuzumab I83E variant in complex with (ac) CQFDA(PH)2STRRLRCGGSK
6B9Z 1.82 Å, Trastuzumab Fab v3
5U5M 1.88 Å, Crystal structure of I83E meditope-enabled trastuzumab with azido-meditope
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
4IOI 1.95 Å, Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC
4HJG 2.0 Å, Meditope-enabled trastuzumab
4HKZ 2.08 Å, Trastuzumab Fab complexed with Protein L and Protein A fragments
6B9Y 2.14 Å, Trastuzumab Fab v3 in complex with 5-phenyl meditope variant
6BAE 2.14 Å, Trastuzumab Fab v3 in complex with CQFDLSTRRLKC
1YMH 2.6 Å, anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W

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