6ULR: HLA class I antigen

Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation. Determined by X-ray diffraction at 3.2 Å resolution. Released 27 May 2020.

Method: X-ray diffraction
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,510
Mol. weight: 94.49 kDa
Released: 27 May 2020

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

Secondary structure: helices and β-sheets

6ULR contains 23 α-helices and 70 β-strands across 5 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, 19 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	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	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-173	9
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	222-223	2	4
β-strand	229-230	2	3
α-helix	232-233	2
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 2 helices, 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	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	50-51	2	6
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	8
β-strand	12-16	5	9
β-strand	21-26	6	8
β-strand	34-41	8	9
β-strand	47-53	7	9
β-strand	58-59	2	8
β-strand	64-66	3	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	88-95	8	9
α-helix	101-103	3
β-strand	109-114	6	9
β-strand	123-128	6	10
β-strand	129	1	11
β-strand	136-141	6	10
α-helix	150-152	3
β-strand	157-159	3	10
β-strand	163-167	5	10
β-strand	172-181	10	10

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	10-14	5	13
β-strand	19-24	6	12
α-helix	25-26	2
β-strand	31-37	7	13
β-strand	43-50	8	13
β-strand	53-57	5	13
β-strand	64-68	5	12
β-strand	74-78	5	12
α-helix	83-85	3
β-strand	87-94	8	13
β-strand	104-105	2	13
β-strand	109-114	6	13
α-helix	117-119	3
β-strand	121	1	14
β-strand	124-128	5	11
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	11
β-strand	151	1	14
β-strand	155-161	7	15
β-strand	164-166	3	15
β-strand	170-172	3	11
β-strand	177-178	2	11
β-strand	188-197	10	11
α-helix	198-201	4
β-strand	207-214	8	15
β-strand	217	1	16
α-helix	228-229	2
β-strand	231	1	16
β-strand	233-240	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I antigen	A	protein	274	Homo sapiens	C1K0Y1 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Gly-ala-asp-gly-val-gly-lys-ser-ala	C	protein	9	Homo sapiens	P01111 (AlphaFold model)
TCR-V-alpha 4*01	D	protein	206	Homo sapiens
TCR-V-beta 5-6*01	E	protein	244	Homo sapiens

Sequence of entity 1 (A), FASTA

>6ULR_1 HLA class I antigen (chains A)
CSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDG
KDYIALNEDLRSWTAADKAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKKTLQ
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW

Sequence of entity 2 (B), FASTA

>6ULR_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6ULR_3 GLY-ALA-ASP-GLY-VAL-GLY-LYS-SER-ALA (chains C)
GADGVGKSA

Sequence of entity 4 (D), FASTA

>6ULR_4 TCR-V-alpha 4*01 (chains D)
MAGLAKTTQPISVDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTN
EVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGDMDQAGTALIFGKGTTLSVSSDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSP

Sequence of entity 5 (E), FASTA

>6ULR_5 TCR-V-beta 5-6*01 (chains E)
MAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNF
PDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLGEGRVDGYTFGSGTRLTVVEDLRNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

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
6UON 3.5 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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