6UON: TCR-V-alpha-12-02*01

Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation. Determined by X-ray diffraction at 3.5 Å resolution. Released 27 May 2020.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 10
Atoms: 13,102
Mol. weight: 188.49 kDa
Released: 27 May 2020

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

Secondary structure: helices and β-sheets

6UON contains 40 α-helices and 143 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: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	23
α-helix	20	1
β-strand	21-28	8	23
β-strand	31-37	7	23
β-strand	46-47	2	23
α-helix	50-52	3
α-helix	57-85	29
β-strand	93-103	11	23
β-strand	109-118	10	23
β-strand	121-126	6	23
β-strand	133-135	3	23
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
α-helix	183-185	3
β-strand	186-193	8	24
β-strand	198-208	11	24
β-strand	214-219	6	25
β-strand	222-223	2	25
β-strand	229-230	2	24
β-strand	234-235	2	24
β-strand	241-250	10	24
α-helix	254-256	3
β-strand	257-262	6	25
β-strand	270-272	3	25

Chains B and E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	26
α-helix	4-5	2
β-strand	6-11	6	27
β-strand	21-30	10	27
β-strand	31	1	26
β-strand	35-41	7	28
β-strand	44-45	2	28
β-strand	50-51	2	27
β-strand	55-56	2	27
β-strand	62-70	9	27
β-strand	78-84	7	28
β-strand	91-94	4	28

Chain D: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	29
α-helix	20	1
β-strand	21-28	8	29
β-strand	31-37	7	29
β-strand	46-47	2	29
α-helix	50-53	4
α-helix	57-85	29
β-strand	93-103	11	29
β-strand	109-118	10	29
β-strand	121-126	6	29
β-strand	133-135	3	29
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	30
α-helix	184-185	2
β-strand	186-193	8	31
β-strand	198-208	11	31
β-strand	209	1	30
β-strand	214-219	6	32
β-strand	229-230	2	31
β-strand	234-235	2	31
β-strand	241-250	10	31
α-helix	254-256	3
β-strand	257-262	6	32
β-strand	270-272	3	32

Chain G: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	11	1	2
β-strand	19-25	7	1
β-strand	32-38	7	3
β-strand	45-50	6	3
β-strand	56-58	3	1
β-strand	61-65	5	1
β-strand	71-76	6	1
β-strand	86-92	7	3
β-strand	99-101	3	3
β-strand	105-106	2	3
β-strand	107	1	2
β-strand	119-124	6	4
β-strand	125	1	5
α-helix	127-129	3
β-strand	132-137	6	4
β-strand	153-155	3	4
α-helix	156-158	3
β-strand	159-163	5	4
β-strand	168-177	10	4
α-helix	184-187	4

Chain H: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	10-14	5	7
β-strand	19-21	3	8
β-strand	23-25	3	6
β-strand	31-37	7	7
β-strand	43-50	8	7
β-strand	56-57	2	7
β-strand	65-66	2	8
β-strand	73	1	6
β-strand	76-78	3	8
β-strand	87-94	8	7
β-strand	101-102	2	7
β-strand	106-111	6	7
α-helix	114-116	3
β-strand	118	1	9
β-strand	121-125	5	5
α-helix	126-128	3
α-helix	129-135	7
β-strand	137-147	11	5
β-strand	148	1	9
β-strand	152-158	7	10
β-strand	161-162	2	10
β-strand	167-169	3	5
α-helix	173	1
β-strand	174-175	2	5
β-strand	185-194	10	5
α-helix	195-199	5
β-strand	204-211	8	10
β-strand	214	1	11
α-helix	225-226	2
β-strand	228	1	11
β-strand	230-237	8	10

Chain I: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	12
β-strand	19-24	6	13
β-strand	32-38	7	14
β-strand	45-50	6	14
β-strand	62-66	5	13
β-strand	71-76	6	13
α-helix	81-83	3
β-strand	86-92	7	14
β-strand	99-101	3	14
β-strand	105-106	2	14
β-strand	108-109	2	12
β-strand	119-123	5	15
β-strand	125	1	16
β-strand	133-137	5	15
β-strand	153-155	3	15
β-strand	172-177	6	15
α-helix	184-187	4
α-helix	189-191	3
β-strand	198	1	15

Chain J: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	17
β-strand	10-14	5	18
β-strand	19-21	3	19
β-strand	23-25	3	17
β-strand	31-37	7	18
β-strand	43-51	9	18
β-strand	54-57	4	18
β-strand	65-66	2	19
β-strand	73	1	17
β-strand	76-78	3	19
β-strand	87-94	8	18
β-strand	101-102	2	18
β-strand	106-111	6	18
α-helix	114-116	3
β-strand	118	1	20
β-strand	121-125	5	16
α-helix	126-128	3
α-helix	129-134	6
β-strand	137-147	11	16
β-strand	148	1	20
β-strand	152-158	7	21
β-strand	161-162	2	21
β-strand	167-169	3	16
α-helix	173	1
β-strand	174-175	2	16
β-strand	185-194	10	16
α-helix	195-199	5
β-strand	204-211	8	21
β-strand	214	1	22
α-helix	225-226	2
β-strand	228	1	22
β-strand	230-237	8	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR-V-alpha-12-02*01	G, I	protein	202	Homo sapiens
TCR-V-beta-10-2*01	H, J	protein	241	Homo sapiens
HLA class I antigen	A, D	protein	274	Homo sapiens	C1K0Y1 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	99	Homo sapiens	P61769 (AlphaFold model)
Gly-ala-asp-gly-val-gly-lys-ser-ala-leu	C, F	protein	10	Homo sapiens	P01111 (AlphaFold model)

Sequence of entity 1 (G, I), FASTA

>6UON_1 TCR-V-alpha-12-02*01 (chains G, I)
MKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDGR
FTAQLNKASQYVSLLIRDSQPSDSATYLCAAAMDSSYKLIFGSGTRLLVRPDIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSP

Sequence of entity 2 (H, J), FASTA

>6UON_2 TCR-V-beta-10-2*01 (chains H, J)
MAGITQSPRYKITETGRQVTLMCHQTWSHSYMFWYRQDLGHGLRLIYYSAAADITDKGEV
PDGYVVSRSKTENFPLTLESATRSQTSVYFCASSDPGTEAFFGQGTRLTVVEDLRNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Sequence of entity 3 (A, D), FASTA

>6UON_3 HLA class I antigen (chains A, D)
CSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDG
KDYIALNEDLRSWTAADKAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKKTLQ
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW

Sequence of entity 4 (B, E), FASTA

>6UON_4 Beta-2-microglobulin (chains B, E)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (C, F), FASTA

>6UON_5 GLY-ALA-ASP-GLY-VAL-GLY-LYS-SER-ALA-LEU (chains C, F)
GADGVGKSAL

Primary citation

High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D. Sim, M.J.W., Lu, J., Spencer, M. et al. Proc Natl Acad Sci U S A (2020) 117:12826-12835. DOI 10.1073/pnas.1921964117 · PubMed

Other PDB entries of the same protein (UniProt C1K0Y1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6ULI 1.88 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
6JTN 1.9 Å, Crystal structure of HLA-C08 in complex with a tumor mut10m peptide
6JTP 1.9 Å, Crystal structure of HLA-C08 in complex with a tumor mut9m peptide
6ULK 1.9 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
6ULN 2.01 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
6ULR 3.2 Å, Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation
9WJ6 4.54 Å, An integrated in silico-in vitro workflow for discovering high-affinity, selective…

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