6JXR: Human T cell receptor-CD3 complex

Structure of human T cell receptor-CD3 complex. Determined by electron microscopy at 3.7 Å resolution. Released 11 Sept 2019.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,437
Mol. weight: 184.05 kDa
Released: 11 Sept 2019

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

Secondary structure: helices and β-sheets

6JXR contains 21 α-helices and 80 β-strands across 8 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-56	28

Chain b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	28-53	26

Chain d: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	1
β-strand	32-36	5	1
β-strand	42-46	5	2
β-strand	50-51	2	1
β-strand	57-62	6	1
β-strand	69-74	6	2
β-strand	83-91	9	2
β-strand	96-98	3	3
α-helix	101-127	27

Chain e: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	35-36	2
β-strand	37-41	5	21
β-strand	44-48	5	21
β-strand	57-61	5	2
β-strand	65-66	2	2
β-strand	75-77	3	21
β-strand	81-85	5	21
β-strand	94-100	7	2
α-helix	105-107	3
β-strand	110-116	7	2
β-strand	122-124	3	3
α-helix	127-153	27

Chain f: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	4
β-strand	44-48	5	4
β-strand	57-60	4	5
β-strand	65-66	2	5
β-strand	75-77	3	4
β-strand	81-85	5	4
β-strand	94-96	3	6
β-strand	97-100	4	5
α-helix	105-107	3
β-strand	111-116	6	6
β-strand	122-123	2	7
α-helix	129-154	26

Chain g: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	8
β-strand	41-46	6	8
β-strand	53-57	5	6
β-strand	60-65	6	6
β-strand	72-76	5	8
β-strand	83-88	6	6
β-strand	93	1	6
β-strand	97-102	6	6
β-strand	108-109	2	7
α-helix	112-136	25

Chain m: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	27-28	2	9
β-strand	33-36	4	10
β-strand	41-46	6	9
β-strand	55-60	6	10
α-helix	65-66	2
β-strand	67-72	6	10
β-strand	76-80	5	9
β-strand	83-88	6	9
β-strand	93-98	6	9
α-helix	103-105	3
β-strand	107-113	7	10
β-strand	121-122	2	10
β-strand	126-131	6	10
β-strand	140-143	4	11
α-helix	144	1
β-strand	145	1	12
α-helix	146	1
β-strand	153-158	6	11
β-strand	174	1	11
α-helix	177-179	3
β-strand	180-184	5	11
β-strand	189-198	10	11
α-helix	205-207	3
α-helix	220-222	3
α-helix	229-232	4
α-helix	240-272	33

Chain n: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	13
β-strand	29-33	5	14
β-strand	38-40	3	15
β-strand	41-44	4	13
β-strand	50	1	16
β-strand	51-57	7	14
β-strand	61-68	8	14
β-strand	74-76	3	14
β-strand	84-85	2	15
β-strand	92	1	13
β-strand	95-97	3	15
α-helix	102-104	3
β-strand	106-110	5	14
β-strand	113	1	16
β-strand	128-133	6	14
β-strand	140	1	17
β-strand	143-147	5	18
β-strand	148	1	12
α-helix	151-156	6
β-strand	159-169	11	18
β-strand	170	1	17
β-strand	176-180	5	19
β-strand	183-184	2	19
β-strand	189-191	3	18
β-strand	207-216	10	18
β-strand	226-233	8	19
β-strand	236	1	20
β-strand	250	1	20
β-strand	252-259	8	19
α-helix	270-307	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD3 zeta chain	a, b	protein	164	Homo sapiens	P20963 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	d	protein	171	Homo sapiens	P04234 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	e, f	protein	207	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	g	protein	182	Homo sapiens	P09693 (AlphaFold model)
T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha constant	m	protein	252	Homo sapiens	A0A0B4J271, A0N4Z6, P01848
T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta…	n	protein	291	Homo sapiens	A0A0K0K1A5, P0DSE2

Sequence of entity 1 (a, b), FASTA

>6JXR_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR

Sequence of entity 2 (d), FASTA

>6JXR_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 3 (e, f), FASTA

>6JXR_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (g), FASTA

>6JXR_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 5 (m), FASTA

>6JXR_5 T cell receptor alpha variable 12-3,Possible J 11 gene segment,T cell receptor alpha constant (chains m)
QQKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQYSRKGPELLMYTYSSGNKEDG
RFTAQVDKSSKYISLFIRDSQPSDSATYLCAMSKGYSTLTFGKGTMLLVSPDIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAG
FNLLMTLRLWSS

Sequence of entity 6 (n), FASTA

>6JXR_6 T cell receptor beta variable 6-5,M1-specific T cell receptor beta chain,T cell receptor beta constant 2 (chains n)
GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEVPN
GYNVSRSTTEDFPLRLLSAAPSQTSVYFCASRRRQGASGEQYFGPGTRLTVTEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPA
LNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
ADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVLMAMVKRKDSRG

Primary citation

Structural basis of assembly of the human T cell receptor-CD3 complex. Zheng, L., Lin, J., Zhang, B. et al. Nature (2019) 573:546-552. DOI 10.1038/s41586-019-1537-0 · 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

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