8ES8: PN45545 TCR-CD3

CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239). Determined by electron microscopy at 2.65 Å resolution. Released 3 May 2023.

Method: Electron microscopy
Resolution: 2.65 Å
Organism: Homo sapiens
Chains: 11
Atoms: 11,976
Mol. weight: 242.05 kDa
Ligands: NAG, Y01
Released: 3 May 2023

Explore 8ES8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ES8 contains 37 α-helices and 110 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: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	11-14	4	10
β-strand	19-21	3	9
β-strand	24-26	3	9
β-strand	32-39	8	11
β-strand	46-52	7	11
β-strand	60-61	2	9
β-strand	64-69	6	9
β-strand	74-79	6	9
α-helix	84-86	3
β-strand	89-96	8	11
β-strand	106-107	2	11
β-strand	111-112	2	11
β-strand	113-116	4	10
α-helix	117	1
β-strand	125-128	4	12
α-helix	129-131	3
β-strand	138-143	6	12
β-strand	159-161	3	12
α-helix	162-164	3
β-strand	165-169	5	12
β-strand	174-183	10	12
β-strand	204	1	12
α-helix	214-219	6
α-helix	225-256	32

Chain B: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	23-25	3	13
β-strand	31-38	8	14
β-strand	42-49	8	14
β-strand	56-57	2	14
β-strand	64-67	4	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	104-105	2	14
β-strand	109-114	6	14
α-helix	117-119	3
β-strand	121	1	16
β-strand	124-128	5	17
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	17
β-strand	151	1	16
β-strand	155-161	7	18
β-strand	164-166	3	18
β-strand	170-172	3	17
β-strand	177-178	2	17
β-strand	188-197	10	17
α-helix	198-201	4
β-strand	207-214	8	18
β-strand	217	1	19
α-helix	228-229	2
β-strand	231	1	19
β-strand	233-240	8	18
α-helix	249-288	40

Chain D: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	26-28	3	1
β-strand	32-36	5	1
α-helix	40-41	2
β-strand	42-46	5	2
β-strand	50-51	2	1
β-strand	57-62	6	1
α-helix	63-65	3
β-strand	68-73	6	2
β-strand	84-91	8	2
β-strand	96-98	3	3
α-helix	101-126	26

Chain E: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	8
β-strand	44-48	5	8
β-strand	57-61	5	2
β-strand	65-66	2	2
β-strand	75-77	3	8
β-strand	81-85	5	8
α-helix	89-92	4
β-strand	94-100	7	2
β-strand	110-116	7	2
β-strand	122-124	3	3
α-helix	127-153	27

Chain F: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	4
β-strand	44-48	5	4
β-strand	57-61	5	5
β-strand	64-66	3	5
β-strand	75-77	3	4
β-strand	81-84	4	4
α-helix	89-92	4
β-strand	94-100	7	5
α-helix	105-107	3
β-strand	111-116	6	5
β-strand	122-123	2	6
α-helix	127-155	29

Chain G: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	7
β-strand	41-46	6	7
β-strand	53-57	5	5
β-strand	60-65	6	5
β-strand	71-76	6	7
α-helix	77-79	3
β-strand	83-88	6	5
α-helix	93-96	4
β-strand	97-102	6	5
β-strand	108-109	2	6
α-helix	112-135	24

Chain M: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	24
β-strand	6-11	6	25
β-strand	21-30	10	25
β-strand	31	1	24
β-strand	36-41	6	26
β-strand	44-45	2	26
β-strand	50-51	2	25
β-strand	55-56	2	25
β-strand	62-70	9	25
β-strand	78-83	6	26
β-strand	91-94	4	26

Chain N: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	20
α-helix	20	1
β-strand	21-28	8	20
β-strand	31-37	7	20
β-strand	46-47	2	20
α-helix	50-54	5
α-helix	57-85	29
β-strand	94-103	10	20
β-strand	109-118	10	20
β-strand	121-126	6	20
β-strand	133-135	3	20
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	21
α-helix	184-185	2
β-strand	186	1	22
β-strand	189-193	5	22
β-strand	198-208	11	22
β-strand	209	1	21
β-strand	214-219	6	23
β-strand	222-223	2	23
β-strand	228-230	3	22
α-helix	231-233	3
β-strand	234-235	2	22
β-strand	241-250	10	22
β-strand	257-262	6	23
β-strand	272-273	2	23

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD3 zeta chain	Y, Z	protein	173	Homo sapiens	P20963 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	D	protein	174	Homo sapiens	P04234 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	E, F	protein	211	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	G	protein	185	Homo sapiens	P09693 (AlphaFold model)
PN45545 TCR alpha chain	A	protein	278	Homo sapiens
PN45545 TCR beta chain	B	protein	319	Homo sapiens
MHC class I antigen	N	protein	277	Homo sapiens	Q861F7
Beta-2-microglobulin	M	protein	100	Homo sapiens	P61769
Melanoma-associated antigen 4	P	protein	10	Homo sapiens	P43358

Sequence of entity 1 (Y, Z), FASTA

>8ES8_1 T-cell surface glycoprotein CD3 zeta chain (chains Y, Z)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRGSGLEVLFQ

Sequence of entity 2 (D), FASTA

>8ES8_2 T-cell surface glycoprotein CD3 delta chain (chains D)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNKGSG

Sequence of entity 3 (E, F), FASTA

>8ES8_3 T-cell surface glycoprotein CD3 epsilon chain (chains E, F)
MGQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILW
QHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVC
ENCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKER
PPPVPNPDYEPIRKGQRDLYSGLNQRRIGSG

Sequence of entity 4 (G), FASTA

>8ES8_4 T-cell surface glycoprotein CD3 gamma chain (chains G)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RNGSG

Sequence of entity 5 (A), FASTA

>8ES8_5 PN45545 TCR alpha chain (chains A)
MSLSSLLKVVTASLWLGPGIAQKITQTQPGMFVQEKEAVTLDCTYDTSDPSYGLFWYKQP
SSGEMIFLIYQGSYDQQNATEGRYSLNFQKARKSANLVISASQLGDSAMYFCAMRGGGSG
GSYIPTFGRGTSLIVHPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVY
ITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKS
FETDTNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Sequence of entity 6 (B), FASTA

>8ES8_6 PN45545 TCR beta chain (chains B)
MGFRLLCCVAFCLLGAGPVDVKVTQSSRYLVKRTGEKVFLECVQDMDHENMFWYRQDPGL
GLRLIYFSYDVKMKEKGDIPEGYSVSREKKERFSLILESASTNQTSMYLCASSFTGPYNS
PLHFGNGTRLTVTEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWV
NGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEND
EWTQDRAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLYAVLVSALV
LMAMVKRKDSRGRAKRGSG

Sequence of entity 7 (N), FASTA

>8ES8_7 MHC class I antigen (chains N)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 8 (M), FASTA

>8ES8_8 Beta-2-microglobulin (chains M)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 9 (P), FASTA

>8ES8_9 Melanoma-associated antigen 4 (chains P)
GVYDGREHTV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
Y01	Cholesterol hemisuccinate	C31 H50 O4	1

Primary citation

Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM. Saotome, K., Dudgeon, D., Colotti, K. et al. Nat Commun (2023) 14:2401-2401. DOI 10.1038/s41467-023-37532-7 · PubMed

Other PDB entries of the same protein (UniProt P20963 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OQ1 1.9 Å, Tandem SH2 domains of ZAP-70 with 19-mer zeta1 peptide
3IK5 2.05 Å, SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80)
4XZ1 2.8 Å, ZAP-70-tSH2:Compound-B adduct
1YGR 2.9 Å, Crystal structure of the tandem phosphatase domain of RPTP CD45
7FJE 3.0 Å, Cryo-EM structure of a membrane protein(LL)
9CI8 3.01 Å, T cell receptor complex
8ES7 3.04 Å, CryoEM structure of PN45545 TCR-CD3 complex
7PHR 3.08 Å, Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I
9JY1 3.08 Å, delta epsilon/delta epsilon Fab-TCR tetramer
7FJF 3.1 Å, Cryo-EM structure of a membrane protein(CS)
8TW6 3.1 Å, TCR in nanodisc ND-II
9IRU 3.14 Å, Cryo-em structure of TCR-4B1 complex

Browse structure collections

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