7ST3: PDB entry 7ST3

Consequences of HLA single chain trimer mutations on peptide presentation and binding affinity. Determined by X-ray diffraction at 2.78 Å resolution. Released 23 Nov 2022.

Method: X-ray diffraction
Resolution: 2.78 Å
Organisms: Human papillomavirus type 16, Pongo pygmaeus, Homo sapiens
Chains: 32
Atoms: 57,837
Mol. weight: 973.05 kDa
Released: 23 Nov 2022

Explore 7ST3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ST3 contains 212 α-helices and 644 β-strands across 32 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: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	8
α-helix	28-29	2
β-strand	30-35	6	9
β-strand	45-54	10	9
β-strand	55	1	8
β-strand	60-65	6	10
β-strand	69	1	10
β-strand	74-75	2	9
α-helix	76-78	3
β-strand	79-80	2	9
β-strand	86-94	9	9
β-strand	102-107	6	10
β-strand	115-118	4	10
β-strand	146-155	10	11
α-helix	163	1
β-strand	164-171	8	11
β-strand	174-180	7	11
β-strand	189-190	2	11
α-helix	194-197	4
α-helix	200-227	28
β-strand	237-246	10	11
β-strand	252-261	10	11
β-strand	264-269	6	11
β-strand	276-278	3	11
α-helix	281-292	12
α-helix	295-301	7
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	12
β-strand	329-333	5	13
β-strand	345-351	7	13
β-strand	352	1	12
β-strand	356-359	4	14
β-strand	372-373	2	13
α-helix	374-376	3
β-strand	377-378	2	13
β-strand	384-389	6	13
β-strand	402-406	5	14
β-strand	413-415	3	14

Chain A: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	1
α-helix	28-29	2
β-strand	30-35	6	2
β-strand	45-54	10	2
β-strand	55	1	1
β-strand	60-65	6	3
β-strand	69	1	3
β-strand	74-75	2	2
α-helix	76-78	3
β-strand	79-80	2	2
β-strand	86-94	9	2
β-strand	102-107	6	3
β-strand	115-118	4	3
β-strand	146-155	10	4
α-helix	163	1
β-strand	164-171	8	4
β-strand	174-180	7	4
β-strand	189-190	2	4
α-helix	193-195	3
α-helix	200-227	28
β-strand	237-246	10	4
β-strand	252-261	10	4
β-strand	264-269	6	4
β-strand	276-278	3	4
α-helix	281-292	12
α-helix	295-301	7
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	5
β-strand	329-333	5	6
β-strand	344-351	8	6
β-strand	352	1	5
β-strand	356-358	3	7
β-strand	372-373	2	6
α-helix	374-376	3
β-strand	377-378	2	6
β-strand	384-390	7	6
β-strand	402-406	5	7
β-strand	413-415	3	7

Chains b, B, D, H, J, L, N, P, R and Z: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	17
β-strand	12-14	3	18
β-strand	20-26	7	17
β-strand	36-41	6	18
β-strand	47-53	7	18
β-strand	59-61	3	18
α-helix	63-65	3
β-strand	69-73	5	17
β-strand	79-84	6	17
α-helix	89-91	3
β-strand	93-100	8	18
β-strand	106-108	3	18
β-strand	112-116	5	18

Chain c: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	26
α-helix	28-29	2
β-strand	30-35	6	27
β-strand	45-54	10	27
β-strand	55	1	26
β-strand	60-65	6	28
β-strand	69	1	28
β-strand	74-75	2	27
β-strand	79-80	2	27
β-strand	86-94	9	27
β-strand	102-107	6	28
β-strand	115-118	4	28
β-strand	146-155	10	29
α-helix	163	1
β-strand	164-171	8	29
β-strand	174-180	7	29
β-strand	189-190	2	29
α-helix	194-197	4
α-helix	200-228	29
β-strand	237-246	10	29
β-strand	252-261	10	29
β-strand	264-269	6	29
β-strand	276-278	3	29
α-helix	281-292	12
α-helix	296-301	6
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	30
β-strand	329-333	5	31
β-strand	344-351	8	31
β-strand	352	1	30
β-strand	356-360	5	32
α-helix	374-376	3
β-strand	377-378	2	31
β-strand	384-390	7	31
β-strand	402-406	5	32
β-strand	413-415	3	32

Chain C: 11 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	19
α-helix	28-29	2
β-strand	30-35	6	20
β-strand	45-54	10	20
β-strand	55	1	19
β-strand	60-65	6	21
β-strand	69	1	21
β-strand	74-75	2	20
α-helix	76-78	3
β-strand	79-80	2	20
β-strand	86-94	9	20
β-strand	102-107	6	21
β-strand	115-118	4	21
β-strand	146-155	10	22
α-helix	163	1
β-strand	164-171	8	22
β-strand	174-180	7	22
β-strand	189-190	2	22
α-helix	194-197	4
α-helix	200-227	28
β-strand	237-246	10	22
β-strand	252-261	10	22
β-strand	264-269	6	22
β-strand	276-278	3	22
α-helix	281-292	12
α-helix	295-301	7
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	23
β-strand	329-332	4	24
β-strand	344-351	8	24
β-strand	352	1	23
β-strand	356-362	7	25
β-strand	371-373	3	24
α-helix	374-376	3
β-strand	377-378	2	24
β-strand	384-390	7	24
β-strand	400-406	7	25
β-strand	413-415	3	25

Chain d: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	35
β-strand	12-14	3	36
β-strand	20-26	7	35
α-helix	30-32	3
β-strand	36-41	6	36
β-strand	47-53	7	36
β-strand	59-61	3	36
α-helix	63-65	3
β-strand	69-73	5	35
β-strand	79-84	6	35
α-helix	89-91	3
β-strand	93-100	8	36
β-strand	106-108	3	36
β-strand	112-116	5	36

Chain e: 12 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	44
α-helix	28-29	2
β-strand	30-35	6	45
β-strand	45-54	10	45
β-strand	55	1	44
β-strand	59-65	7	46
β-strand	69	1	46
β-strand	74-75	2	45
α-helix	76-78	3
β-strand	79-80	2	45
β-strand	86-94	9	45
β-strand	102-108	7	46
β-strand	115-118	4	46
β-strand	146-155	10	47
α-helix	163	1
β-strand	164-171	8	47
β-strand	174-180	7	47
β-strand	189-190	2	47
α-helix	194-197	4
α-helix	200-227	28
β-strand	237-246	10	47
β-strand	252-261	10	47
β-strand	264-269	6	47
β-strand	276-278	3	47
α-helix	281-292	12
α-helix	295-301	7
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	48
α-helix	327-328	2
β-strand	329-333	5	49
β-strand	345-351	7	49
β-strand	352	1	48
β-strand	356-361	6	50
β-strand	372-373	2	49
α-helix	374-376	3
β-strand	377-378	2	49
β-strand	384-389	6	49
β-strand	401-406	6	50
β-strand	413-415	3	50

Chain E: 11 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	37
α-helix	28-29	2
β-strand	30-35	6	38
β-strand	45-54	10	38
β-strand	55	1	37
β-strand	60-65	6	39
β-strand	69	1	39
β-strand	74-75	2	38
α-helix	76-78	3
β-strand	79-80	2	38
β-strand	86-94	9	38
β-strand	102-107	6	39
β-strand	115-118	4	39
β-strand	146-155	10	40
α-helix	163	1
β-strand	164-171	8	40
β-strand	174-180	7	40
β-strand	189-190	2	40
α-helix	193-195	3
α-helix	200-227	28
β-strand	237-246	10	40
β-strand	252-261	10	40
β-strand	264-269	6	40
β-strand	276-278	3	40
α-helix	281-292	12
α-helix	295-301	7
α-helix	302-306	5
α-helix	307-317	11
α-helix	319-322	4
β-strand	326	1	41
β-strand	329-333	5	42
β-strand	343-351	9	42
β-strand	352	1	41
β-strand	356-362	7	43
β-strand	365-366	2	43
β-strand	371-373	3	42
α-helix	374-376	3
β-strand	377-378	2	42
β-strand	384-391	8	42
β-strand	400-406	7	43
β-strand	413-415	3	43

14 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera	A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c, e	protein	429	Human papillomavirus type 16, Pongo pygmaeus, Homo sapiens	A0A678ZGP6 (AlphaFold model), P03129 (AlphaFold model), P16213 (AlphaFold model)
VHH	B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f	protein	116	Lama glama

Sequence of entity 1 (A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c, e), FASTA

>7ST3_1 Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera (chains A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c, e)
YMLDLQPETTDLYCGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFH
PSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPK
IVKWDRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQ
FVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGCYNQSEAGS
HTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMCAQTTKHKWEAAHV
AEQLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAE
ITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTL
RWEHHHHHH

Sequence of entity 2 (B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f), FASTA

>7ST3_2 VHH (chains B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f)
EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYG
DSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSS

Primary citation

Effects of HLA single chain trimer design on peptide presentation and stability. Finton, K.A.K., Rupert, P.B., Friend, D.J. et al. Front Immunol (2023) 14:1170462-1170462. DOI 10.3389/fimmu.2023.1170462 · PubMed

Other PDB entries of the same protein (UniProt A0A678ZGP6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7STG 2.7 Å, Consequences of HLA single chain trimer mutations on peptide presentation and binding…
7SSH 2.73 Å, Single chain trimer HLA-A*02:01 (Y108A) with HPV.16 E7 peptide YMLDLQPETTDLYC

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