7NDU: Gag:02 TCR

Gag:02 TCR in complex with HLA-E featuring a non-natural amino acid. Determined by X-ray diffraction at 2.9 Å resolution. Released 26 Jan 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 5
Atoms: 6,545
Mol. weight: 94.88 kDa
Released: 26 Jan 2022

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

Secondary structure: helices and β-sheets

7NDU contains 25 α-helices and 77 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	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	138-145	8
α-helix	148-152	5
α-helix	155-158	4
α-helix	159-164	6
α-helix	165-174	10
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	229-230	2	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	270-272	3	4

Chain BBB: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	6	1	5
β-strand	9-11	3	5
β-strand	21-22	2	6
β-strand	23-30	8	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	5
α-helix	52-54	3
β-strand	55-56	2	5
β-strand	62-67	6	5
β-strand	69-70	2	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain DDD: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	10-11	2	9
β-strand	14	1	10
β-strand	16	1	11
β-strand	19-24	6	8
β-strand	38-44	7	9
α-helix	49-50	2
β-strand	51-56	6	9
β-strand	66-67	2	8
β-strand	77-79	3	8
β-strand	86-91	6	8
β-strand	94	1	11
β-strand	100-107	8	9
α-helix	109-112	4
β-strand	123-124	2	9
β-strand	127	1	10
β-strand	136-141	6	12
β-strand	142	1	13
β-strand	149-154	6	12
β-strand	171-172	2	12
α-helix	173-175	3
β-strand	177-179	3	14
β-strand	186-188	3	14
β-strand	189-193	5	12

Chain EEE: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	10-14	5	16
β-strand	15	1	17
β-strand	17	1	17
β-strand	19-24	6	15
β-strand	38-44	7	16
α-helix	50	1
β-strand	51-57	7	16
β-strand	64-68	5	16
β-strand	76-79	4	15
β-strand	87-91	5	15
β-strand	100-107	8	16
β-strand	117-118	2	16
β-strand	122-127	6	16
α-helix	131-133	3
β-strand	135	1	18
α-helix	136-138	3
β-strand	139-142	4	13
α-helix	143-145	3
α-helix	146-152	7
β-strand	154-164	11	13
β-strand	165	1	18
β-strand	169-175	7	19
β-strand	178-179	2	19
β-strand	184-186	3	13
β-strand	191-192	2	13
α-helix	200-201	2
β-strand	202-211	10	13
α-helix	212-215	4
β-strand	221-228	8	19
β-strand	231	1	20
α-helix	242-243	2
β-strand	245	1	20
β-strand	247-254	8	19

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(276-284 H4C)	CCC	protein	9	Human immunodeficiency virus 1
T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor…	DDD	protein	199	Homo sapiens	A0A075B6U7, A0A0B4J268 (AlphaFold model), P0DSE1
T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr beta chain	EEE	protein	244	Homo sapiens	A0A0J9YX06, K7N5M4, P04435

Sequence of entity 1 (AAA), FASTA

>7NDU_1 HLA class I histocompatibility antigen, alpha chain E (chains AAA)
MGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEY
WDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQCAYD
GKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETL
LHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (BBB), FASTA

>7NDU_2 Beta-2-microglobulin (chains BBB)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (CCC), FASTA

>7NDU_3 Gag6V(276-284 H4C) (chains CCC)
RMYSPVSIL

Sequence of entity 4 (DDD), FASTA

>7NDU_4 T cell receptor alpha variable 4,T cell receptor alpha joining 23,M1-specific T cell receptor alpha chain (chains DDD)
MLAKTTQPISMDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTNEV
ASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGSSFNQGGKLIFGQGTELSVKPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDT

Sequence of entity 5 (EEE), FASTA

>7NDU_5 T cell receptor beta variable 7-9,T cell receptor beta joining 1-2,Human nkt tcr 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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