9C3E: TCR - CD3 complex

TCR - CD3 complex bound to HLA. Determined by electron microscopy at 3.5 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 9
Atoms: 10,619
Mol. weight: 277.36 kDa
Ligands: NAG, CLR
Released: 2 Oct 2024

Explore 9C3E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C3E contains 31 α-helices and 106 β-strands across 9 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: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
β-strand	30-33	4	2
β-strand	38-44	7	1
β-strand	49	1	3
β-strand	53-57	5	2
β-strand	64-68	5	2
β-strand	75-78	4	1
β-strand	81-86	6	1
β-strand	91-96	6	1
α-helix	101-103	3
β-strand	105-111	7	2
β-strand	113	1	3
β-strand	122-123	2	2
β-strand	127-132	6	2
β-strand	141-145	5	4
β-strand	146	1	5
α-helix	147-148	2
β-strand	154-159	6	4
β-strand	175-177	3	4
β-strand	181-185	5	4
β-strand	190-199	10	4
β-strand	220	1	4
α-helix	230-234	5
α-helix	241-270	30

Chain B: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	6
β-strand	29-33	5	7
β-strand	38-44	7	6
β-strand	50-57	8	7
β-strand	61-68	8	7
β-strand	75	1	7
β-strand	84-85	2	6
β-strand	92-97	6	6
α-helix	102-104	3
β-strand	107-113	7	7
β-strand	121-123	3	7
β-strand	127-132	6	7
β-strand	139	1	8
β-strand	142-146	5	9
β-strand	147	1	5
α-helix	148-149	2
α-helix	150-156	7
β-strand	158-168	11	9
β-strand	169	1	8
β-strand	173-179	7	10
β-strand	182-183	2	10
β-strand	188-190	3	9
α-helix	194	1
β-strand	195-196	2	9
β-strand	206-215	10	9
α-helix	216-219	4
β-strand	225-232	8	10
β-strand	235	1	11
α-helix	246-247	2
β-strand	249	1	11
β-strand	251-258	8	10
α-helix	267-293	27

Chain D: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	26-27	2	12
α-helix	29-31	3
β-strand	32-36	5	12
β-strand	41-46	6	13
β-strand	50-51	2	12
β-strand	57-62	6	12
α-helix	63-65	3
β-strand	69-73	5	13
α-helix	77-79	3
β-strand	84-91	8	13
β-strand	96-98	3	14
α-helix	101-124	24

Chain E: 3 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	59-61	3	13
β-strand	64-66	3	13
β-strand	75-77	3	15
β-strand	81-85	5	15
β-strand	94-98	5	13
α-helix	105-107	3
β-strand	110-116	7	13
β-strand	122-124	3	14
α-helix	127-149	23

Chain F: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	39-41	3	16
β-strand	44-48	5	16
β-strand	58-61	4	17
β-strand	65-66	2	17
β-strand	75-77	3	16
β-strand	81-84	4	16
β-strand	94-99	6	17
α-helix	105-107	3
β-strand	112-115	4	17
β-strand	123	1	18
α-helix	127-152	26

Chain G: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	32-34	3	19
β-strand	41-45	5	19
β-strand	53-57	5	20
β-strand	60-65	6	20
β-strand	72-76	5	19
α-helix	77-79	3
β-strand	83-85	3	17
β-strand	86-88	3	20
β-strand	97-101	5	17
β-strand	108	1	18
α-helix	112-136	25

Chain H: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	123	1	21
β-strand	126-130	5	22
β-strand	144-148	5	22
β-strand	151	1	21
β-strand	156-160	5	23
β-strand	171	1	22
β-strand	176	1	24
β-strand	182	1	24
β-strand	183-186	4	22
β-strand	199-203	5	23
β-strand	211-214	4	23
β-strand	327-336	10	25
β-strand	345-352	8	25
β-strand	355-361	7	25
β-strand	370	1	25
α-helix	381-408	28
β-strand	418-427	10	25
β-strand	433-442	10	25
β-strand	445-448	4	25
α-helix	470-474	5
α-helix	476-485	10
α-helix	487-498	12
α-helix	500-503	4
β-strand	510-514	5	26
β-strand	526-532	7	26
β-strand	538-541	4	27
β-strand	558-559	2	26
β-strand	565-570	6	26
β-strand	583-586	4	27
β-strand	587	1	28
β-strand	590	1	28

Chain X: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
α-helix	30-45	16

1 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
TCRa	A	protein	272	Homo sapiens	P01848 (AlphaFold model)
TCRb (EGFP fusion)	B	protein	557	Homo sapiens	P0DTU4 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	D	protein	125	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	194	Homo sapiens	P09693
T-cell surface glycoprotein CD3 zeta chain	X, Y	protein	164	Homo sapiens	P20963
Cancer/testis antigen 1,Beta-2-microglobulin,MHC class I antigen	H	protein	593	Homo sapiens	H9BNV4, P61769, P78358

Sequence of entity 1 (A), FASTA

>9C3E_1 TCRa (chains A)
METLLGLLILWLQLQWVSSKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPG
KGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVRPLYGGSYI
PTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDK
TVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETD
TNLNFQNLSVIGFRILLLKVAGFNLLMTLRLW

Sequence of entity 2 (B), FASTA

>9C3E_2 TCRb (EGFP fusion) (chains B)
MSIGLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGM
GLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGE
LFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVN
GKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDE
WTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVL
MAMVKRKDSRGVEDTMGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLT
LKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDD
GNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKV
NFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEF
VTAAGITLGMDELYKVD

Sequence of entity 3 (D), FASTA

>9C3E_3 T-cell surface glycoprotein CD3 delta chain (chains D)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCF

Sequence of entity 4 (E, F), FASTA

>9C3E_4 T-cell surface glycoprotein CD3 epsilon chain (chains E, F)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 5 (G), FASTA

>9C3E_5 T-cell surface glycoprotein CD3 gamma chain (chains G)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RNVEHHHHHHHHVD

Sequence of entity 6 (X, Y), FASTA

>9C3E_6 T-cell surface glycoprotein CD3 zeta chain (chains X, Y)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR

Sequence of entity 7 (H), FASTA

>9C3E_7 Cancer/testis antigen 1,Beta-2-microglobulin,MHC class I antigen (chains H)
SLLMWITQVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXI
QRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWS
FYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQ
RMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQL
RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKP

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8
CLR	Cholesterol	C27 H46 O	2

Primary citation

The resting and ligand-bound states of the membrane-embedded human T-cell receptor-CD3 complex. Notti, R.Q., Yi, F., Heissel, S. et al. Nat Commun (2025) 16:10996-10996. DOI 10.1038/s41467-025-66939-7 · PubMed

Other PDB entries of the same protein (UniProt P01848 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UDT 1.35 Å, T cell receptor (TRAV22,TRBV7-9) structure
4WW1 1.38 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
2BNU 1.4 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
1KGC 1.5 Å, Immune Receptor
2BNQ 1.7 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2BNR 1.9 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2IAL 1.92 Å, Structural basis for recognition of mutant self by a tumor-specific, MHC class…
5C0C 1.97 Å, 1E6 TCR in complex with HLA-A02 carrying RQFGPDWIVA
2VLM 1.98 Å, The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are…
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
7RYL 2.0 Å, T cell receptor CO3

Browse structure collections

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