7SQP: PDB entry 7SQP

Single chain trimer HLA-A*02:01 (Y108C) with HPV.16 E7 peptide YMLDLQPETTDL. Determined by X-ray diffraction at 2.53 Å resolution. Released 23 Nov 2022.

Method: X-ray diffraction
Resolution: 2.53 Å
Organisms: Human papillomavirus type 16, Pongo pygmaeus, Homo sapiens
Chains: 4
Atoms: 7,611
Mol. weight: 120.97 kDa
Released: 23 Nov 2022

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

Secondary structure: helices and β-sheets

7SQP contains 29 α-helices and 80 β-strands across 4 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: 12 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
α-helix	327-328	2
β-strand	329-336	8	6
β-strand	341-351	11	6
β-strand	352	1	5
β-strand	357-361	5	7
β-strand	371-373	3	6
α-helix	374-376	3
β-strand	377-378	2	6
β-strand	384-393	10	6
β-strand	401-405	5	7
β-strand	413-415	3	7

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	8
β-strand	12-14	3	9
β-strand	20-26	7	8
α-helix	30-32	3
β-strand	36-41	6	9
β-strand	47-53	7	9
β-strand	59-61	3	9
α-helix	63-65	3
β-strand	69-74	6	8
β-strand	79-84	6	8
α-helix	89-91	3
β-strand	93-100	8	9
β-strand	106-108	3	9
β-strand	112-116	5	9

Chain C: 12 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	10
α-helix	28-29	2
β-strand	30-35	6	11
β-strand	45-54	10	11
β-strand	55	1	10
β-strand	60-65	6	12
β-strand	69	1	12
β-strand	74-75	2	11
α-helix	76-78	3
β-strand	79-80	2	11
β-strand	86-94	9	11
β-strand	102-107	6	12
β-strand	115-118	4	12
β-strand	146-155	10	13
α-helix	163	1
β-strand	164-171	8	13
β-strand	174-180	7	13
β-strand	189-190	2	13
α-helix	193-195	3
α-helix	200-227	28
β-strand	237-246	10	13
β-strand	252-261	10	13
β-strand	264-269	6	13
β-strand	276-278	3	13
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	14
α-helix	327-328	2
β-strand	329-336	8	15
β-strand	342-351	10	15
β-strand	352	1	14
β-strand	356-361	6	16
β-strand	371-373	3	15
α-helix	374-376	3
β-strand	377-378	2	15
β-strand	384-392	9	15
β-strand	401-406	6	16
β-strand	413-415	3	16

Chain D: 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
α-helix	30-32	3
β-strand	36-41	6	18
β-strand	47-53	7	18
β-strand	59-61	3	18
β-strand	69-74	6	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera	A, C	protein	427	Human papillomavirus type 16, Pongo pygmaeus, Homo sapiens	A0A6S7XV52 (AlphaFold model), P03129 (AlphaFold model), P16213 (AlphaFold model)
VHH	B, D	protein	116	Homo sapiens

Sequence of entity 1 (A, C), FASTA

>7SQP_1 Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera (chains A, C)
YMLDLQPETTDLGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPS
DIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIV
KWDRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFV
RFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGAYNQSEAGSHT
VQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAE
QLRAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEIT
LTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRW
EHHHHHH

Sequence of entity 2 (B, D), FASTA

>7SQP_2 VHH (chains B, D)
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 A0A6S7XV52 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SR5 2.35 Å, Single chain trimer HLA-A*02:01 (Y108C, A163C) with Wilms tumor protein peptide RMFPNAPYL
7SR3 2.49 Å, Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPETTDL
7SR0 2.54 Å, Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPET
7SR4 2.59 Å, Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPETTDLYC
9NFB 3.23 Å, Structure of the cross-HLA supertype antibody R302 bound to a class I MHC presenting a…

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