7SRK: PDB entry 7SRK

Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF. Determined by X-ray diffraction at 2.5 Å resolution. Released 23 Nov 2022.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Homo sapiens, Pongo pygmaeus, Lama glama
Chains: 4
Atoms: 7,685
Mol. weight: 119.77 kDa
Released: 23 Nov 2022

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

Secondary structure: helices and β-sheets

7SRK contains 29 α-helices and 83 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: 13 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	1
α-helix	28-29	2
β-strand	30-35	6	2
β-strand	43	1	3
β-strand	45-54	10	2
β-strand	55	1	1
β-strand	60-65	6	4
β-strand	68-69	2	4
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	4
β-strand	115-118	4	4
β-strand	146-155	10	5
α-helix	163	1
β-strand	164-171	8	5
β-strand	174-180	7	5
β-strand	189-190	2	5
α-helix	193-195	3
α-helix	200-227	28
β-strand	237-246	10	5
β-strand	252-261	10	5
β-strand	264-269	6	5
β-strand	276-278	3	5
α-helix	281-292	12
α-helix	295-302	8
α-helix	303-307	5
α-helix	308-317	10
α-helix	319-322	4
β-strand	326	1	6
α-helix	327-328	2
β-strand	329-335	7	7
β-strand	341-351	11	7
β-strand	352	1	6
β-strand	357-359	3	8
β-strand	371-373	3	7
α-helix	374-376	3
β-strand	377-378	2	7
β-strand	384-393	10	7
α-helix	397-399	3
β-strand	403-405	3	8
β-strand	413-414	2	8

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	9
β-strand	12-14	3	10
β-strand	20-27	8	9
β-strand	33-41	9	10
β-strand	47-53	7	10
β-strand	59-61	3	10
α-helix	63-65	3
β-strand	69-74	6	9
β-strand	79-84	6	9
α-helix	89-91	3
β-strand	93-101	9	10
β-strand	106-108	3	10
β-strand	112-116	5	10

Chain C: 11 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	27	1	11
α-helix	28-29	2
β-strand	30-35	6	12
β-strand	43	1	9
β-strand	45-54	10	12
β-strand	55	1	11
β-strand	60-65	6	13
β-strand	68-69	2	13
β-strand	74-75	2	12
α-helix	76-78	3
β-strand	79-80	2	12
β-strand	86-94	9	12
β-strand	102-107	6	13
β-strand	115-118	4	13
β-strand	146-155	10	14
α-helix	163	1
β-strand	164-171	8	14
β-strand	174-180	7	14
β-strand	189-190	2	14
α-helix	193-195	3
α-helix	200-227	28
β-strand	237-246	10	14
β-strand	252-261	10	14
β-strand	264-269	6	14
β-strand	276-278	3	14
α-helix	281-292	12
α-helix	295-304	10
α-helix	306-317	12
α-helix	319-322	4
β-strand	326	1	15
β-strand	329-336	8	16
β-strand	341-351	11	16
β-strand	352	1	15
β-strand	357-362	6	17
β-strand	365-366	2	17
β-strand	371-373	3	16
α-helix	374-376	3
β-strand	377-378	2	16
β-strand	384-393	10	16
α-helix	397-399	3
β-strand	400-405	6	17
β-strand	413-415	3	17

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	3
β-strand	12-13	2	18
β-strand	20-28	9	3
α-helix	30-32	3
β-strand	33-41	9	18
β-strand	47-53	7	18
β-strand	59-61	3	18
α-helix	63-65	3
β-strand	69-74	6	3
β-strand	79-84	6	3
α-helix	89-91	3
β-strand	93-101	9	18
β-strand	106-108	3	18
β-strand	112-115	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera	A, C	protein	423	Homo sapiens, Pongo pygmaeus	F6IR24 (AlphaFold model), P16213 (AlphaFold model), Q6NSI4 (AlphaFold model)
VHH	B, D	protein	116	Lama glama

Sequence of entity 1 (A, C), FASTA

>7SRK_1 RPA-related protein RADX peptide,Beta-2-microglobulin,MHC class I antigen chimera (chains A, C)
YPPVPETFGGGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEV
DLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDR
DMGGGGSGGGGSGGGGSGGGGSGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDS
DAASQRMEPRAPWIEQEGPEYWDEETGKVKAHSQTDRENLRIALRCYNQSEAGSHTLQMM
FGCDVGSDGRFLRGYHQYAYDGKDYIALKEDLRSWTAADMCAQITKRKWEAAHVAEQQRA
YLEGTCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQ
RDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEHHH
HHH

Sequence of entity 2 (B, D), FASTA

>7SRK_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 F6IR24 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8EK5 2.11 Å, Engineered scFv 10LH bound to PHOX2B/HLA-A24:02
8HN4 2.85 Å, Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI

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