9RU5: TCRpub/pMHC

Cryo-EM structure of TCRpub/pMHC. Determined by electron microscopy at 3.26 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 4
Atoms: 4,825
Mol. weight: 83.44 kDa
Released: 13 Aug 2025

Explore 9RU5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RU5 contains 15 α-helices and 56 β-strands across 3 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: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	9-10	2	2
β-strand	20	1	3
β-strand	23	1	1
β-strand	32-37	6	2
β-strand	43-49	7	2
β-strand	55-57	3	3
α-helix	59-61	3
β-strand	63-65	3	3
β-strand	67	1	1
β-strand	72	1	1
β-strand	75-76	2	3
α-helix	82-84	3
β-strand	86-95	10	2
β-strand	101-104	4	2
β-strand	109-111	3	2
β-strand	123-127	5	4
β-strand	136	1	5
β-strand	137-141	5	4
α-helix	160-162	3
β-strand	165-167	3	6
β-strand	172-174	3	6
β-strand	181	1	5
β-strand	202	1	4

Chain B: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	7
β-strand	8-12	5	8
β-strand	17-21	5	7
β-strand	29-36	8	8
β-strand	40-48	9	8
β-strand	52-55	4	8
β-strand	62-66	5	7
β-strand	72-76	5	7
α-helix	81-83	3
β-strand	85-92	8	8
β-strand	103	1	8
β-strand	107-112	6	8
α-helix	115-117	3
β-strand	119	1	9
β-strand	122-126	5	10
α-helix	127-129	3
α-helix	130-136	7
β-strand	139-146	8	10
β-strand	149	1	9
β-strand	153-157	5	11
β-strand	158-159	2	12
β-strand	162-163	2	12
β-strand	168-170	3	10
α-helix	174	1
β-strand	175	1	13
α-helix	176	1
β-strand	187	1	13
β-strand	190-194	5	10
β-strand	207-212	6	11
β-strand	215	1	14
β-strand	229	1	14
β-strand	231-236	6	11

Chain M: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	15
α-helix	18	1
β-strand	19-21	3	15
β-strand	24-25	2	15
β-strand	32	1	15
β-strand	45	1	15
α-helix	48-50	3
α-helix	55-82	28
β-strand	93-101	9	15
β-strand	107-116	10	15
β-strand	123-124	2	16
β-strand	131-132	2	16
α-helix	138-147	10
α-helix	150-158	9
α-helix	161-172	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCRpub alpha chain	A	protein	209	Homo sapiens
TCRpub beta chain	B	protein	242	Homo sapiens
MHC class I antigen	M	protein	276	Homo sapiens	F6IQR9 (AlphaFold model)
ORF3a protein	P	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9RU5_1 TCRpub alpha chain (chains A)
QSVAQPEDQVNVAEGNPLTVKCTYSVSGNPYLFWYVQYPNRGLQFLLKYITGDNLVKGSY
GFEAEFNKSQTSFHLKKPSALVSDSALYFCAVRVVTSGGSYIPTFGRGTSLIVHPYIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>9RU5_2 TCRpub beta chain (chains B)
GVTQTPRYLIKTRGQQVTLSCSPISGHRSVSWYQQTPGQGLQFLFEYFSETQRNKGNFPG
RFSGRQFSNSRSEMNVSTLELGDSALYLCASSLAGDLGTEAFFGQGTRLTVVEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Sequence of entity 3 (M), FASTA

>9RU5_3 MHC class I antigen (chains M)
HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYWDQ
ETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDGKD
YIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQRT
DPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ
KWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWELSS

Sequence of entity 4 (P), FASTA

>9RU5_4 ORF3a protein (chains P)
FTSDYYQLY

Primary citation

Cryo-EM structure of TCRpub/pMHC. Akil, C., Zhu, Y., Hardenbrook, N. et al. To be published.

Other PDB entries of the same protein (UniProt F6IQR9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YIV 2.1 Å, N17.1.2 recognition of NRAS neoantigens
8YJ2 2.26 Å, N17.1.2 recognition of NRAS neoantigens
8T7R 3.84 Å, Crystal structure of human leukocyte antigen A*0101 in complex with the Fab of…

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