8ES9: PN45428 TCR-CD3

CryoEM structure of PN45428 TCR-CD3 in complex with HLA-A2 MAGEA4. Determined by electron microscopy at 3.25 Å resolution. Released 3 May 2023.

Method: Electron microscopy
Resolution: 3.25 Å
Organism: Homo sapiens
Chains: 11
Atoms: 11,844
Mol. weight: 240.27 kDa
Ligands: Y01, NAG
Released: 3 May 2023

Explore 8ES9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ES9 contains 35 α-helices and 108 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: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	18-25	8	1
β-strand	32-38	7	2
β-strand	45-49	5	2
β-strand	56-58	3	1
β-strand	62-66	5	1
β-strand	70-76	7	1
β-strand	85-91	7	2
β-strand	102-103	2	2
β-strand	108-112	5	2
β-strand	121-124	4	3
α-helix	125-127	3
β-strand	134-139	6	3
α-helix	148-150	3
β-strand	155-157	3	3
α-helix	158-160	3
β-strand	161-165	5	3
β-strand	170-179	10	3
β-strand	200	1	3
α-helix	210-215	6
α-helix	221-251	31

Chain B: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	4
β-strand	7	1	5
β-strand	10-14	5	6
β-strand	19-22	4	5
β-strand	25	1	4
β-strand	32-37	6	7
β-strand	38	1	6
β-strand	45-51	7	7
β-strand	57-58	2	7
β-strand	67-69	3	5
β-strand	78-81	4	5
α-helix	86-88	3
β-strand	91	1	6
β-strand	94-97	4	7
α-helix	103-104	2
β-strand	105-106	2	7
β-strand	111-115	5	6
β-strand	122	1	8
β-strand	125-129	5	9
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	9
β-strand	152	1	8
β-strand	156-162	7	10
β-strand	165-166	2	10
β-strand	171-173	3	9
β-strand	178-179	2	9
β-strand	189-198	10	9
α-helix	199-202	4
β-strand	208-215	8	10
β-strand	218	1	11
β-strand	232	1	11
β-strand	234-241	8	10
α-helix	250-288	39

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	12
β-strand	32-36	5	12
α-helix	40-41	2
β-strand	42-46	5	13
β-strand	50-51	2	12
β-strand	57-62	6	12
β-strand	68-73	6	13
β-strand	84-91	8	13
β-strand	96-98	3	14
α-helix	101-126	26

Chain E: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	19
β-strand	44-48	5	19
β-strand	57-61	5	13
β-strand	65-66	2	13
β-strand	75-77	3	19
β-strand	81-85	5	19
α-helix	89-92	4
β-strand	94-100	7	13
β-strand	110-116	7	13
β-strand	122-124	3	14
α-helix	127-154	28

Chain F: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	15
β-strand	44-48	5	15
β-strand	57-61	5	16
β-strand	64-66	3	16
β-strand	75-77	3	15
β-strand	81-85	5	15
α-helix	89-92	4
β-strand	94-100	7	16
α-helix	105-107	3
β-strand	111-116	6	16
β-strand	122-123	2	17
α-helix	127-155	29

Chain G: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	18
β-strand	41-45	5	18
β-strand	53-57	5	16
β-strand	60-65	6	16
β-strand	72-76	5	18
α-helix	77-79	3
β-strand	83-88	6	16
α-helix	93-96	4
β-strand	97-102	6	16
β-strand	108-109	2	17
α-helix	112-135	24

Chain M: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	23
β-strand	6-11	6	24
β-strand	21-30	10	24
β-strand	31	1	23
β-strand	35-41	7	25
β-strand	44-45	2	25
β-strand	50-51	2	24
β-strand	55-56	2	24
β-strand	62-70	9	24
β-strand	78-84	7	25
β-strand	91-94	4	25

Chain N: 10 helices, 18 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	50-52	3
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	139-148	10
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	186	1	21
β-strand	189-193	5	21
β-strand	198-208	11	21
β-strand	213-219	7	22
β-strand	222-223	2	22
β-strand	228-230	3	21
α-helix	231-233	3
β-strand	234-235	2	21
β-strand	241-250	10	21
α-helix	254-256	3
β-strand	257-263	7	22
β-strand	272	1	22

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
PN45428 TCR alpha chain	A	protein	274	Homo sapiens
PN45428 TCR beta chain	B	protein	320	Homo sapiens
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)
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 (A), FASTA

>8ES9_1 PN45428 TCR alpha chain (chains A)
MSLSSLLKVVTASLWLGPGIEDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDP
GKGPEFLFTLYSAGEEKEKERLKATLTKKESFLHITAPKPEDSATYLCAVQPLNAGNNRK
LIWGLGTSLAVNPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDK
TVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETD
TNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Sequence of entity 2 (B), FASTA

>8ES9_2 PN45428 TCR beta chain (chains B)
MGFRLLCCVAFCLLGAGPVGAVVSQHPSWVICKSGTSVKIECRSLDFQATTMFWYRQFPK
QSLMLMATSNEGSKATYEQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSAREWGG
TEAFFGQGTRLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWW
VNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEN
DEWTQDRAKPVTQIVSAEAWGRADCGFTSVSYQQGVLSATILYEILLGKATLYAVLVSAL
VLMAMVKRKDSRGRAKRGSG

Sequence of entity 3 (Y, Z), FASTA

>8ES9_3 T-cell surface glycoprotein CD3 zeta chain (chains Y, Z)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRGSGLEVLFQ

Sequence of entity 4 (D), FASTA

>8ES9_4 T-cell surface glycoprotein CD3 delta chain (chains D)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNKGSG

Sequence of entity 5 (E, F), FASTA

>8ES9_5 T-cell surface glycoprotein CD3 epsilon chain (chains E, F)
MGQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILW
QHNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVC
ENCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKER
PPPVPNPDYEPIRKGQRDLYSGLNQRRIGSG

Sequence of entity 6 (G), FASTA

>8ES9_6 T-cell surface glycoprotein CD3 gamma chain (chains G)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RNGSG

Sequence of entity 7 (N), FASTA

>8ES9_7 MHC class I antigen (chains N)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 8 (M), FASTA

>8ES9_8 Beta-2-microglobulin (chains M)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 9 (P), FASTA

>8ES9_9 Melanoma-associated antigen 4 (chains P)
GVYDGREHTV

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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)
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
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

Browse structure collections

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