8EK5: Engineered scFv 10LH

Engineered scFv 10LH bound to PHOX2B/HLA-A24:02. Determined by X-ray diffraction at 2.11 Å resolution. Released 6 Dec 2023.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,216
Mol. weight: 95.14 kDa
Released: 6 Dec 2023

Explore 8EK5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EK5 contains 19 α-helices and 54 β-strands across 3 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
α-helix	21	1
β-strand	22-29	8	1
β-strand	32-38	7	1
β-strand	47-48	2	1
α-helix	51-55	5
α-helix	58-86	29
β-strand	95-104	10	1
β-strand	110-119	10	1
β-strand	122-127	6	1
β-strand	134-136	3	1
α-helix	139-150	12
α-helix	153-160	8
α-helix	161-165	5
α-helix	166-175	10
α-helix	177-180	4
β-strand	184	1	2
α-helix	185-186	2
β-strand	187-194	8	3
β-strand	199-209	11	3
β-strand	210	1	2
β-strand	215-220	6	4
β-strand	223-225	3	4
β-strand	229-231	3	3
α-helix	232-234	3
β-strand	235-236	2	3
β-strand	242-251	10	3
α-helix	255-257	3
β-strand	258-263	6	4
β-strand	271-273	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain E: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	115	1	8
β-strand	119-122	4	9
β-strand	128-133	6	8
α-helix	135-138	4
β-strand	143-147	5	9
β-strand	154-157	4	9
β-strand	158	1	10
β-strand	162	1	10
α-helix	163-164	2
β-strand	171-176	6	8
β-strand	179-184	6	8
α-helix	189-191	3
β-strand	193-200	8	9
β-strand	208-210	3	9
β-strand	214-218	5	9
β-strand	243-247	5	11
β-strand	251-252	2	12
β-strand	258-265	8	11
α-helix	269-271	3
β-strand	274-279	6	13
β-strand	285-291	7	13
β-strand	298-300	3	13
β-strand	308-313	6	11
α-helix	314-316	3
β-strand	318-323	6	11
α-helix	328-330	3
β-strand	332-340	9	13
β-strand	345-349	5	13
β-strand	353-355	3	13
β-strand	356-357	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	277	Homo sapiens	F6IR24 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Paired mesoderm homeobox protein 2B peptide	C	protein	9	Homo sapiens	Q99453 (AlphaFold model)
10LH single chain fragment variable (scFv)	E	protein	464	Homo sapiens

Sequence of entity 1 (A), FASTA

>8EK5_1 MHC class I antigen (chains A)
MGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETL
QRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>8EK5_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8EK5_3 Paired mesoderm homeobox protein 2B peptide (chains C)
QYNPIRTTF

Sequence of entity 4 (E), FASTA

>8EK5_4 10LH single chain fragment variable (scFv) (chains E)
HHHHHHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGR
TLSDYNIQKESTLHLVLRLRGGMALPVTALLLPLALLLHAARPSRNGGDGQSVLTQPPSV
SVSPGQTASITCSGDSLGNKYACWYQQKPGQSPVLVIYQDSKRPSGIPERFSGSNSGNTA
TLTISGTQAMDEADYYCQAWDSSRGYTVVFGTGTKVTVSSQTGGSGGGGSGGGGSGGGGS
EVQLLESGGGLVQPGGSLRLSCAASGFTFDSYAMSWVRQAPGKGLEWVSAISGYGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKYTYFLDAFDIWGQGTMVTVSSP
SFVKKVDPSYLMLPGESARLHCKLKGSPVIQVTWFKNNKELSESNTVRMYFVNSEAILDI
TDVKVEDSGSYSCEAVNDVGSDSCSTEIVGLNDIFEAQKIEWHE

Primary citation

Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Sun, Y., Florio, T.J., Gupta, S. et al. Sci Immunol (2023) 8:eadj5792-eadj5792. DOI 10.1126/sciimmunol.adj5792 · PubMed

Other PDB entries of the same protein (UniProt F6IR24 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SRK 2.5 Å, Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF
8HN4 2.85 Å, Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI

Browse structure collections

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