6L9L: H2-Ld a1a2

1D4 TCR recognition of H2-Ld a1a2 A5 Peptide Complexes. Determined by X-ray diffraction at 2.4 Å resolution. Released 18 Nov 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 8
Atoms: 10,177
Mol. weight: 140.92 kDa
Released: 18 Nov 2020

Explore 6L9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L9L contains 35 α-helices and 99 β-strands across 6 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	57-85	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	152-158	7
α-helix	159-164	6
α-helix	165-173	9

Chain C: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	2
β-strand	8-12	5	3
α-helix	15-16	2
β-strand	17-22	6	2
β-strand	30-37	8	3
β-strand	44-49	6	3
β-strand	54-55	2	2
β-strand	60-63	4	2
β-strand	69-74	6	2
α-helix	79-81	3
β-strand	83-91	9	3
β-strand	99	1	4
β-strand	102-107	6	3
β-strand	116-121	6	5
β-strand	122	1	6
β-strand	129-134	6	5
α-helix	142-145	4
β-strand	150-152	3	5
α-helix	153-155	3
β-strand	156-160	5	5
β-strand	165-174	10	5
α-helix	181-184	4
β-strand	195	1	5

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	7
β-strand	8-12	5	4
β-strand	17-23	7	7
β-strand	29-36	8	4
β-strand	40-47	8	4
β-strand	54-55	2	4
β-strand	63-65	3	7
β-strand	71-76	6	7
α-helix	81-83	3
β-strand	85-92	8	4
β-strand	99-100	2	4
β-strand	104-109	6	4
α-helix	112-114	3
β-strand	116	1	8
β-strand	119-123	5	6
α-helix	124-126	3
α-helix	127-133	7
β-strand	135-145	11	6
β-strand	146	1	8
β-strand	150-156	7	9
β-strand	159-161	3	9
β-strand	165-167	3	6
β-strand	172-173	2	6
β-strand	183-192	10	6
α-helix	193-197	5
β-strand	202-209	8	9
β-strand	212	1	10
α-helix	223-224	2
β-strand	226	1	10
β-strand	228-235	8	9

Chain E: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
α-helix	19-20	2
β-strand	21-28	8	11
β-strand	31-37	7	11
β-strand	46-47	2	11
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	11
β-strand	109-118	10	11
β-strand	121-126	6	11
β-strand	133-135	3	11
α-helix	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-173	9

Chain G: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
β-strand	8-12	5	13
α-helix	15-16	2
β-strand	17-22	6	12
β-strand	30-37	8	13
β-strand	44-49	6	13
β-strand	54-55	2	12
β-strand	60-63	4	12
β-strand	69-74	6	12
α-helix	79-81	3
β-strand	83-91	9	13
β-strand	99	1	14
β-strand	102-107	6	13
β-strand	116-122	7	15
β-strand	129-134	6	15
α-helix	142-145	4
β-strand	150-152	3	15
α-helix	153-155	3
β-strand	156-160	5	15
β-strand	165-174	10	15
α-helix	181-184	4
β-strand	195	1	15

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	16
β-strand	8-12	5	14
β-strand	17-23	7	16
β-strand	29-36	8	14
β-strand	40-47	8	14
β-strand	54-55	2	14
β-strand	63-65	3	16
β-strand	71-76	6	16
α-helix	81-83	3
β-strand	85-92	8	14
β-strand	99-100	2	14
β-strand	104-109	6	14
α-helix	112-114	3
β-strand	116	1	17
β-strand	119-124	6	15
α-helix	125-126	2
α-helix	127-133	7
β-strand	135-145	11	15
β-strand	146	1	17
β-strand	150-156	7	18
β-strand	159-161	3	18
β-strand	165-167	3	15
β-strand	172-173	2	15
β-strand	183-192	10	15
α-helix	193-197	5
β-strand	202-209	8	18
β-strand	212	1	19
α-helix	223-224	2
β-strand	226	1	19
β-strand	228-235	8	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H2-Ld a1a2	A, E	protein	175	Homo sapiens	P01897 (AlphaFold model)
T Cell Receptor	C, G	protein	198	Homo sapiens
T Cell Receptor	D, H	protein	239	Homo sapiens
Ser-pro-ser-tyr-ala-tyr-his-gln-phe	B, F	protein	9	Homo sapiens

Sequence of entity 1 (A, E), FASTA

>6L9L_1 H2-Ld a1a2 (chains A, E)
GPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYW
ERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDG
CDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG

Sequence of entity 2 (C, G), FASTA

>6L9L_2 T Cell Receptor (chains C, G)
AKTTQPDSMESTEGETVHLPCSHATISGNEYIYWYRQVPLQGPEYVTHGLQQNTTNSMAF
LAIASDRKSSTLILTHVSLRDAAVYHCILQGTGSKLSFGKGAKLTVSPDIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFPS

Sequence of entity 3 (D, H), FASTA

>6L9L_3 T Cell Receptor (chains D, H)
AVTQSPRNKVTVTGGNVTLSCRQTNSHNYMYWYRQDTGHGLRLIHYSYGAGNLQIGDVPD
GYKATRTTQEDFFLLLELASPSQTSLYFCASSDGDYEQYFGPGTRLTVLEDLKNVFPPEV
AVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALND
SRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Sequence of entity 4 (B, F), FASTA

>6L9L_4 SER-PRO-SER-TYR-ALA-TYR-HIS-GLN-PHE (chains B, F)
SPSYAYHQF

Primary citation

Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer. Wei, P., Jordan, K.R., Buhrman, J.D. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2100588118 · PubMed

Other PDB entries of the same protein (UniProt P01897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
6L9K 1.8 Å, H2-Ld a1a2 complexed with A5 peptide
8D5N 1.8 Å, Crystal structure of Ld-HF10
3VJ6 1.9 Å, Structure of the MHC class Ib molecule Qa-1b
4MS8 1.92 Å, 42F3 TCR pCPB9/H-2Ld Complex
3ERY 1.95 Å, Different thermodynamic binding mechanisms and peptide fine specificities associated…
5VCL 2.05 Å, Structure of the Qdm peptide bound to Qa-1a
3TJH 2.12 Å, 42F3-p3A1/H2-Ld complex
2OI9 2.35 Å, Structure of the 2C/Ld/QL9 allogeneic complex

Browse structure collections

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