7PB2: JDI TCR

Crystal structure of JDI TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide (VVVGADGVGK). Determined by X-ray diffraction at 3.41 Å resolution. Released 20 Jul 2022.

Method: X-ray diffraction
Resolution: 3.41 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,801
Mol. weight: 189.95 kDa
Released: 20 Jul 2022

Explore 7PB2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PB2 contains 38 α-helices and 152 β-strands across 10 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: 7 helices, 19 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	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	122-126	5	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-195	10	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-249	9	3
β-strand	257-262	6	4
β-strand	272	1	4

Chains B and G: 1 helix, 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	23-30	8	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-68	7	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-6	5
β-strand	8	1	8

Chain D: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	10-14	5	10
β-strand	19-21	3	9
β-strand	24-26	3	9
β-strand	33-39	7	10
β-strand	46-52	7	10
β-strand	58-61	4	9
β-strand	64-69	6	9
β-strand	74-79	6	9
α-helix	84-86	3
β-strand	88-96	9	10
β-strand	104-107	4	10
β-strand	111-116	6	10
α-helix	117-118	2
β-strand	125-130	6	11
β-strand	131	1	12
β-strand	138-143	6	11
β-strand	159-161	3	11
α-helix	162-164	3
β-strand	165	1	11
β-strand	178-183	6	11

Chains E and J: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	22-25	4	13
β-strand	31-37	7	14
β-strand	43-51	9	14
β-strand	54-57	4	14
β-strand	65-67	3	15
β-strand	73	1	13
β-strand	75-78	4	15
α-helix	83-85	3
β-strand	87-94	8	14
β-strand	96	1	8
β-strand	99	1	8
α-helix	102-104	3
β-strand	105-106	2	14
β-strand	110-115	6	14
α-helix	118-120	3
β-strand	122	1	16
β-strand	125-129	5	12
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	12
β-strand	152	1	16
β-strand	156-162	7	17
β-strand	165-167	3	17
β-strand	171-173	3	12
α-helix	177	1
β-strand	178-179	2	12
β-strand	189-198	10	12
α-helix	199-203	5
β-strand	208-215	8	17
β-strand	218	1	18
β-strand	232	1	18
β-strand	234-241	8	17

Chain F: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	19
β-strand	21-28	8	19
β-strand	31-37	7	19
β-strand	46-47	2	19
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	19
β-strand	109-118	10	19
β-strand	121-126	6	19
β-strand	133-135	3	19
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
α-helix	183-185	3
β-strand	186-195	10	20
β-strand	198-208	11	20
β-strand	214-219	6	21
β-strand	222-223	2	21
β-strand	228-230	3	20
β-strand	234-235	2	20
β-strand	241-249	9	20
β-strand	257-262	6	21
β-strand	272	1	21

Chain H: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	8	1	25

Chain I: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	26
β-strand	10-14	5	27
β-strand	19-21	3	26
β-strand	24-26	3	26
β-strand	33-39	7	27
β-strand	46-52	7	27
β-strand	58-61	4	26
β-strand	64-69	6	26
β-strand	74-79	6	26
α-helix	84-86	3
β-strand	88-96	9	27
β-strand	104-107	4	27
β-strand	111-116	6	27
α-helix	117-118	2
β-strand	125-130	6	28
β-strand	131	1	29
β-strand	138-143	6	28
β-strand	159-161	3	28
α-helix	162-164	3
β-strand	165-167	3	28
β-strand	176-183	8	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, F	protein	276	Homo sapiens	A0A583ZB34 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
KRAS G12D peptide (VVVGADGVGK)	C, H	protein	10	Homo sapiens	P01111 (AlphaFold model)
TCR alpha	D, I	protein	203	Homo sapiens
TCR beta	E, J	protein	245	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>7PB2_1 MHC class I antigen (chains A, F)
GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>7PB2_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>7PB2_3 KRAS G12D peptide (VVVGADGVGK) (chains C, H)
VVVGADGVGK

Sequence of entity 4 (D, I), FASTA

>7PB2_4 TCR alpha (chains D, I)
AQKVTQAQTEISVVEKEDVTLDCVYETRDTTYYLFWYKQPPSGELVFLIRRNSFDEQNEI
SGRYSWNFQKSTSSFNFTITASQVVDSAVYFCALSGPSGAGSYQLTFGKGTKLSVIPNIQ
NPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAV
AWSNKSDFACANAFNNSIIPEDT

Sequence of entity 5 (E, J), FASTA

>7PB2_5 TCR beta (chains E, J)
NAGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEV
PDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASSYGPGQHNSPLHFGNGTRLTVTEDLNK
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Primary citation

Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen. Poole, A., Karuppiah, V., Hartt, A. et al. Nat Commun (2022) 13:5333. DOI 10.1038/s41467-022-32811-1

Other PDB entries of the same protein (UniProt A0A583ZB34 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OW4 1.81 Å, Crystal structure of HLA-A*11:01 in complex with KRAS G12D peptide (VVVGADGVGK)
8RYN 1.97 Å, Structure of S2 TCR in complex with HLA-A*11:01 bound to ELFSYLIEK peptide
8WTE 2.17 Å, Crystal structure of TCR in complex with HLA-A*11:01 bound to KRAS-G12V peptide…
8WUL 2.36 Å, Crystal structure of affinity enhanced TCR in complex with HLA-A*11:01 bound to…
7OW3 2.46 Å, Crystal structure of HLA-A*11:01 in complex with KRAS peptide (VVVGAGGVGK)
8RYQ 2.49 Å, Structure of S8-9F3 TCR in complex with HLA-A*11:01 bound to ELFSYLIEK peptide
7OW5 2.58 Å, Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS peptide (VVVGAGGVGK)
7OW6 2.64 Å, Crystal structure of a TCR in complex with HLA-A*11:01 bound to KRAS G12D peptide…

Browse structure collections

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