8RLU: TCR

TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 S3N peptide. Determined by X-ray diffraction at 2.35 Å resolution. Released 16 Oct 2024.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Homo sapiens, Hepatitis B virus
Chains: 10
Atoms: 13,115
Mol. weight: 188.25 kDa
Released: 16 Oct 2024

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

Secondary structure: helices and β-sheets

8RLU contains 50 α-helices and 145 β-strands across 8 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	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222	1	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chains B and G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	11-14	4	9
β-strand	19-25	7	8
β-strand	30-38	9	9
β-strand	45-50	6	9
β-strand	54-58	5	8
β-strand	61-66	6	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-93	9	9
β-strand	100-102	3	9
β-strand	106-111	6	9
α-helix	112-114	3
β-strand	120-125	6	10
β-strand	126	1	11
β-strand	133-138	6	10
α-helix	147-149	3
β-strand	154-156	3	10
α-helix	157-159	3
β-strand	160-164	5	10
α-helix	165-167	3
β-strand	169-178	10	10

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	31-37	7	13
β-strand	43-49	7	13
β-strand	56-57	2	13
β-strand	64-66	3	14
β-strand	73	1	12
β-strand	76-78	3	14
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	102-103	2	13
β-strand	107-112	6	13
α-helix	115-117	3
β-strand	119	1	15
α-helix	120-121	2
β-strand	122-126	5	11
α-helix	127-129	3
α-helix	130-136	7
β-strand	138-148	11	11
β-strand	149	1	15
β-strand	153-159	7	16
β-strand	162-164	3	16
β-strand	168-170	3	11
α-helix	174	1
β-strand	175-176	2	11
β-strand	186-195	10	11
α-helix	196-200	5
β-strand	205-212	8	16
β-strand	215	1	17
β-strand	229	1	17
β-strand	231-238	8	16

Chain F: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	18
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	19
α-helix	184-185	2
β-strand	186-193	8	20
β-strand	198-208	11	20
β-strand	209	1	19
β-strand	214-219	6	21
β-strand	228-230	3	20
α-helix	231-233	3
β-strand	234-235	2	20
β-strand	241-250	10	20
α-helix	254-256	3
β-strand	257-262	6	21
β-strand	270-272	3	21

Chain I: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	25
β-strand	11-14	4	26
β-strand	19-25	7	25
β-strand	30-38	9	26
β-strand	45-50	6	26
β-strand	54-58	5	25
β-strand	61-66	6	25
β-strand	71-76	6	25
α-helix	81-83	3
β-strand	85-93	9	26
β-strand	100-102	3	26
β-strand	106-111	6	26
α-helix	112-114	3
β-strand	120-124	5	27
β-strand	134-138	5	27
β-strand	155-156	2	27
α-helix	157-159	3
β-strand	160-164	5	27
β-strand	169-177	9	27

Chain J: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-14	5	29
β-strand	19-21	3	30
β-strand	22-25	4	28
β-strand	31-37	7	29
β-strand	43-49	7	29
β-strand	56-57	2	29
β-strand	64-66	3	30
β-strand	73	1	28
β-strand	76-78	3	30
α-helix	83-85	3
β-strand	87-94	8	29
β-strand	102-103	2	29
β-strand	107-112	6	29
α-helix	115-117	3
β-strand	119	1	31
α-helix	120-121	2
β-strand	122-126	5	32
α-helix	130-136	7
β-strand	138-148	11	32
β-strand	149	1	31
β-strand	153-157	5	33
β-strand	158-159	2	34
β-strand	162-163	2	34
β-strand	168-170	3	32
α-helix	174	1
β-strand	175-176	2	32
β-strand	186-195	10	32
α-helix	196-198	3
β-strand	208-212	5	33
β-strand	215	1	35
α-helix	226-227	2
β-strand	229	1	35
β-strand	231-235	5	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A, F	protein	276	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Large envelope protein	C, H	protein	9	Hepatitis B virus	Q67953
T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5	D, I	protein	199	Homo sapiens	A0A075B6T6 (AlphaFold model), P0DTU3
T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5	E, J	protein	243	Homo sapiens	A0A0K0K1A5, P0DTU4

Sequence of entity 1 (A, F), FASTA

>8RLU_1 HLA class I histocompatibility antigen, alpha chain E (chains A, F)
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDG
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (B, G), FASTA

>8RLU_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>8RLU_3 Large envelope protein (chains C, H)
ILNPFLPLL

Sequence of entity 4 (D, I), FASTA

>8RLU_4 T cell receptor alpha variable 12-2,T cell receptor alpha chain MC.7.G5 (chains D, I)
MAKEVEQNSGPLSVPEGAIASLNCTYSDRGSVSFFWYRQYSGKSPELIMSIYLNGLKEDG
RFTAQLNKASQYVSLLIRDSQPSDSATYLCAVGNHNTGNMLTFGGGTRLMVKPHIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDT

Sequence of entity 5 (E, J), FASTA

>8RLU_5 T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5 (chains E, J)
MNAGVTQTPKFQVLKTGQSMTLQCAQDMNYEYMSWYRQDPGMGLRLIHYSVSAGLTDQGE
VPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASHRNRLTEAFFGQGTRLTVVEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

Viral sequence determines HLA-E-restricted T cell recognition of hepatitis B surface antigen. Murugesan, G., Paterson, R.L., Kulkarni, R. et al. Nat Commun (2024) 15:10126-10126. DOI 10.1038/s41467-024-54378-9 · PubMed

Other PDB entries of the same protein (UniProt P13747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P4B 1.72 Å, HLA-E*01:03 in complex with IL9
7BH8 1.8 Å, 3H4-Fab HLA-E-VL9 co-complex
7P49 2.05 Å, HLA-E*01:03 in complex with Mtb14
6GH1 2.1 Å, HLA-E*01:03 in complex with Mtb44
9NW7 2.1 Å, CA117v2v8 Fab bound to HLA-E-VL9
6GH4 2.16 Å, HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
6ZKX 2.17 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
8RLT 2.25 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide
6ZKW 2.26 Å, Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)
6ZKZ 2.3 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C)
9NW8 2.3 Å, CA117v2v8 Fab bound to HLA-E-Mtb44
9NW9 2.3 Å, CA117v2v8 Fab bound to HLA-E-RL9HIV

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