7NDQ: Gag:02 TCR

Gag:02 TCR in complex with HLA-E. Determined by X-ray diffraction at 2.55 Å resolution. Released 26 Jan 2022.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 5
Atoms: 6,573
Mol. weight: 94.89 kDa
Released: 26 Jan 2022

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

Secondary structure: helices and β-sheets

7NDQ contains 26 α-helices and 73 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 AAA: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	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	50-54	5
α-helix	57-85	29
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	151-153	3
α-helix	155-157	3
α-helix	158-164	7
α-helix	165-179	15
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	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	253-256	4
β-strand	257-262	6	4
β-strand	270-273	4	4

Chain BBB: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6	1	6
β-strand	9-11	3	7
β-strand	21-30	10	7
β-strand	31	1	5
β-strand	35-41	7	8
β-strand	45	1	8
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-84	7	8
α-helix	90	1
β-strand	91-94	4	8

Chain DDD: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	9
β-strand	10-14	5	10
β-strand	19-24	6	9
β-strand	38-44	7	10
α-helix	49-50	2
β-strand	51-56	6	10
β-strand	66-67	2	9
β-strand	77-79	3	9
β-strand	86-91	6	9
β-strand	101-107	7	10
α-helix	109-112	4
β-strand	122-127	6	10
β-strand	138-141	4	11
β-strand	142	1	12
β-strand	149-152	4	11
β-strand	154	1	13
β-strand	170-172	3	11
β-strand	178-180	3	14
α-helix	181-183	3
β-strand	185-187	3	14
β-strand	189	1	13
β-strand	192-194	3	11

Chain EEE: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	10-14	5	16
β-strand	19-24	6	15
α-helix	25-26	2
β-strand	38-44	7	16
α-helix	49-50	2
β-strand	51-57	7	16
β-strand	64-68	5	16
β-strand	77-79	3	15
α-helix	81-84	3
β-strand	87-91	5	15
β-strand	100-108	9	16
β-strand	114-118	5	16
β-strand	122-127	6	16
α-helix	131-133	3
β-strand	135	1	17
α-helix	136-137	2
β-strand	138-142	5	12
α-helix	143-145	3
α-helix	146-151	6
β-strand	154-164	11	12
β-strand	165	1	17
β-strand	169-175	7	18
β-strand	178-180	3	18
β-strand	184-186	3	12
β-strand	191-192	2	12
α-helix	200-201	2
β-strand	202-211	10	12
α-helix	212-215	4
β-strand	221-228	8	18
β-strand	231	1	19
α-helix	242-243	2
β-strand	245	1	19
β-strand	248-254	7	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	AAA	protein	277	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	BBB	protein	100	Homo sapiens	P61769 (AlphaFold model)
Gag6V	CCC	protein	9	Human immunodeficiency virus 1	B6S6I4
TCR Gag:02-alpha,TCR Gag:02-alpha,TCR Gag:02-alpha	DDD	protein	199	Homo sapiens	A0A075B6U7, A0A0B4J268, P0DSE1
T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta…	EEE	protein	244	Homo sapiens	A0A0J9YX06, K7N5M4, P04435

Sequence of entity 1 (AAA), FASTA

>7NDQ_1 HLA class I histocompatibility antigen, alpha chain E (chains AAA)
MGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEY
WDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYD
GKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETL
LHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (BBB), FASTA

>7NDQ_2 Beta-2-microglobulin (chains BBB)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (CCC), FASTA

>7NDQ_3 Gag6V (chains CCC)
RMYSPVSIL

Sequence of entity 4 (DDD), FASTA

>7NDQ_4 TCR Gag:02-alpha,TCR Gag:02-alpha,TCR Gag:02-alpha (chains DDD)
MLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEV
ASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGSSFNQGGKLIFGQGTELSVKPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDT

Sequence of entity 5 (EEE), FASTA

>7NDQ_5 T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain,T cell receptor beta variable 7-9,M1-specific T cell receptor beta chain (chains EEE)
MDTGVSQNPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSR
LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLGREYGYTFGSGTRLTVVEDLNKV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Primary citation

Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. Barber, C., De Souza, V.A., Paterson, R.L. et al. Eur J Immunol (2022) 52:618-632. DOI 10.1002/eji.202149745 · 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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