9IRS: TCR-OKT3 complex

Cryo-EM structure of the TCR-OKT3 complex. Determined by electron microscopy at 3.18 Å resolution. Released 21 Jan 2026.

Method: Electron microscopy
Resolution: 3.18 Å
Organism: Homo sapiens
Chains: 12
Atoms: 14,979
Mol. weight: 284 kDa
Ligands: CLR
Released: 21 Jan 2026

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

Secondary structure: helices and β-sheets

9IRS contains 39 α-helices and 168 β-strands across 12 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	30-53	24

Chain b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-53	25

Chain d: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	23-25	3
β-strand	26-27	2	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	68-74	7	2
β-strand	83-91	9	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	39-40	2	22
β-strand	44-48	5	22
β-strand	57-61	5	2
β-strand	65-66	2	2
β-strand	76-77	2	22
β-strand	81-85	5	22
β-strand	95-100	6	2
α-helix	105-107	3
β-strand	111-116	6	2
β-strand	122-124	3	3
α-helix	127-153	27

Chain f: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	37-40	4	4
β-strand	44-48	5	4
β-strand	58-61	4	5
β-strand	64-66	3	5
β-strand	75-76	2	4
β-strand	81-85	5	4
β-strand	94-99	6	5
β-strand	111-116	6	5
β-strand	122-124	3	6
α-helix	129-155	27

Chain g: 2 helices, 9 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	72-76	5	7
α-helix	77-79	3
β-strand	82-88	7	5
β-strand	93	1	5
β-strand	97-102	6	5
β-strand	107-109	3	6
α-helix	112-137	26

Chain H: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	23
β-strand	10-12	3	24
β-strand	18-25	8	23
α-helix	29-31	3
β-strand	34-39	6	25
β-strand	45-51	7	25
β-strand	58-60	3	25
α-helix	62-64	3
β-strand	68-73	6	23
β-strand	78-83	6	23
α-helix	88-90	3
β-strand	93-100	8	25
β-strand	105-108	4	25
β-strand	113-114	2	25
β-strand	115-117	3	24
β-strand	123	1	26
β-strand	126-130	5	27
β-strand	142-151	10	27
β-strand	152	1	26
β-strand	159-160	2	28
β-strand	169-171	3	27
α-helix	172-174	3
β-strand	175	1	27
β-strand	181-183	3	27
β-strand	185-189	5	27
β-strand	200-205	6	28
β-strand	210-215	6	28

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	29
β-strand	10-13	4	30
β-strand	18-24	7	29
β-strand	33-37	5	30
β-strand	44-47	4	30
β-strand	61-66	6	29
β-strand	69-75	7	29
α-helix	79-81	3
β-strand	84-89	6	30
α-helix	95	1
β-strand	96-97	2	30
β-strand	101-105	5	30
β-strand	110	1	31
β-strand	113-117	5	32
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-136	9	32
β-strand	138	1	33
β-strand	139	1	31
β-strand	144-149	6	34
β-strand	152	1	34
β-strand	158-162	5	32
α-helix	164-166	3
β-strand	172	1	33
β-strand	174-181	8	32
α-helix	182-185	4
β-strand	190-196	7	34
β-strand	207-209	3	34

4 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	a, b	protein	165	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)
CD3-a	m	protein	272	Homo sapiens
CD3-b	n	protein	312	Homo sapiens
OKT3-H	H, S	protein	219	Homo sapiens
OKT3-L	L, T	protein	213	Homo sapiens

Sequence of entity 1 (a, b), FASTA

>9IRS_1 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRS

Sequence of entity 2 (d), FASTA

>9IRS_2 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 3 (e, f), FASTA

>9IRS_3 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (g), FASTA

>9IRS_4 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 5 (m), FASTA

>9IRS_5 CD3-a (chains m)
MKSLRVLLVILWLQLSWVWSQQKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQY
SRKGPELLMYTYSSGNKEDGRFTAQVDKSSKYISLFIRDSQPSDSATYLCAMSKGYSTLT
FGKGTMLLVSPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTV
LDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN
LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Sequence of entity 6 (n), FASTA

>9IRS_6 CD3-b (chains n)
MSISLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGM
GLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASRRRQGASG
EQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWV
NGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEND
EWTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALV
LMAMVKRKDSRG

Sequence of entity 7 (H, S), FASTA

>9IRS_7 OKT3-H (chains H, S)
QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNY
NQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSSA
KTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

Sequence of entity 8 (L, T), FASTA

>9IRS_8 OKT3-L (chains L, T)
QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAH
FRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEINRADTAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2

Primary citation

Cryo-EM structure of the TCR-OKT3 complex. Li, X., Zhu, Y., Huang, Z. To be published.

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

About this viewer

MolViewer shows 9IRS directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.