6ULN: HLA class I antigen

Molecular basis for tumor infiltrating TCR recognition of hotspot KRAS-G12D mutation. Determined by X-ray diffraction at 2.01 Å resolution. Released 27 May 2020.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,972
Mol. weight: 95.23 kDa
Ligands: MG
Released: 27 May 2020

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

Secondary structure: helices and β-sheets

6ULN contains 30 α-helices and 69 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 A: 12 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	50-53	4
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	159-163	5
α-helix	164-174	11
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	214-218	5	4
β-strand	223	1	4
α-helix	225-227	3
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	258-262	5	4
β-strand	270-273	4	4

Chain B: 3 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
α-helix	52-54	3
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 D: 5 helices, 15 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	48-53	6	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	87-95	9	9
α-helix	101-103	3
β-strand	109-114	6	9
β-strand	123-129	7	10
β-strand	136-141	6	10
α-helix	150-152	3
β-strand	157-159	3	10
α-helix	160-162	3
β-strand	163-167	5	10
α-helix	168-170	3
β-strand	172-181	10	10

Chain E: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
α-helix	25-26	2
β-strand	31-37	7	12
β-strand	44-50	7	12
β-strand	53-57	5	12
β-strand	64-68	5	11
β-strand	74-78	5	11
α-helix	83-85	3
β-strand	87-94	8	12
β-strand	103-104	2	12
β-strand	108-113	6	12
α-helix	116-118	3
β-strand	120	1	13
α-helix	121-122	2
β-strand	123-128	6	10
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	10
β-strand	150	1	13
β-strand	154-160	7	14
β-strand	163-165	3	14
β-strand	169-171	3	10
α-helix	175	1
β-strand	176-177	2	10
β-strand	187-196	10	10
α-helix	197-200	4
β-strand	206-213	8	14
β-strand	216	1	15
α-helix	221-222	2
α-helix	227-228	2
β-strand	230	1	15
β-strand	232-239	8	14

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	243	Homo sapiens

Sequence of entity 1 (A), FASTA

>6ULN_1 HLA class I antigen (chains A)
CSHSMRYFYTAVSRPGRGEPRFIAVGYVDDTQFVQFDSDAASPRGEPRAPWVEQEGPEYW
DRETQKYKRQAQTDRVSLRNLRGYYNQSEAGSHTLQRMYGCDLGPDGRLLRGYNQFAYDG
KDYIALNEDLRSWTAADKAAQITQRKWEAAREAEQRRAYLEGTCVEWLRRYLENGKKTLQ
RAEHPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPLTLRW

Sequence of entity 2 (B), FASTA

>6ULN_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6ULN_3 GLY-ALA-ASP-GLY-VAL-GLY-LYS-SER-ALA (chains C)
GADGVGKSA

Sequence of entity 4 (D), FASTA

>6ULN_4 TCR-V-alpha-4*01 (chains D)
MAGLAKTTQPISVDSYEGQEVNITCSHNNIATNDYITWYQQFPSQGPRFIIQGYKTKVTN
EVASLFIPADRKSSTLSLPRVSLSDTAVYYCLVGDMDQAGTALIFGKGTTLSVSSDIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSP

Sequence of entity 5 (E), FASTA

>6ULN_5 TCR-V-beta-5-6*01 (chains E)
MAGVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNF
PDRFSGHQFPNYSSELNVNALLLGDSALYLCASSLGQTNYGYTFGSGTRLTVVEDLRNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

Water and common crystallization additives (SO4, GOL) are not listed.

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
6ULR 3.2 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…

Browse structure collections

About this viewer

MolViewer shows 6ULN directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.