9IRU: TCR-4B1 complex

Cryo-em structure of TCR-4B1 complex. Determined by electron microscopy at 3.14 Å resolution. Released 21 Jan 2026.

Method: Electron microscopy
Resolution: 3.14 Å
Organism: Homo sapiens
Chains: 10
Atoms: 11,681
Mol. weight: 243.06 kDa
Ligands: CLR
Released: 21 Jan 2026

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

Secondary structure: helices and β-sheets

9IRU contains 36 α-helices and 123 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-53	25

Chain A: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	30-32	3	2
β-strand	39-45	7	1
β-strand	53-58	6	3
β-strand	65-68	4	3
β-strand	69	1	4
β-strand	73	1	4
β-strand	82-87	6	1
β-strand	90-95	6	1
β-strand	105-110	6	3
α-helix	116	1
β-strand	117	1	5
β-strand	118	1	3
β-strand	123-125	3	2
β-strand	134-138	5	6
α-helix	139-141	3
α-helix	142-145	4
β-strand	149-157	9	6
β-strand	165-170	6	7
β-strand	174	1	7
β-strand	179-183	5	6
α-helix	185-187	3
β-strand	194-202	9	6
α-helix	203-206	4
β-strand	211-217	7	7
β-strand	225-230	6	7

Chain b: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	32-53	22

Chain B: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	8
β-strand	29	1	9
β-strand	37-40	4	10
β-strand	41	1	8
α-helix	48-50	3
β-strand	51-58	8	5
β-strand	65-71	7	5
β-strand	76-79	4	5
α-helix	81-83	3
β-strand	89-92	4	10
β-strand	97-102	6	10
β-strand	112-119	8	5
β-strand	129	1	5
β-strand	133-134	2	5
β-strand	135	1	9
β-strand	143	1	11
β-strand	146-150	5	12
α-helix	151-153	3
β-strand	161-171	11	12
β-strand	172	1	11
β-strand	176-180	5	13
β-strand	190-191	2	12
β-strand	202-211	10	12
α-helix	212-214	3
β-strand	215	1	14
β-strand	218	1	14
β-strand	221-226	6	13
α-helix	227-229	3
β-strand	231-236	6	13

Chain d: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	15
β-strand	32-36	5	15
α-helix	40-41	2
β-strand	42-46	5	16
β-strand	50-51	2	15
β-strand	57-62	6	15
α-helix	63-65	3
β-strand	68-74	7	16
β-strand	83-92	10	16
β-strand	96-98	3	17
α-helix	101-123	23

Chain e: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-40	4	18
β-strand	44-48	5	18
β-strand	57-61	5	16
β-strand	65-66	2	16
β-strand	81-85	5	18
β-strand	94-100	7	16
α-helix	105-107	3
β-strand	111-117	7	16
β-strand	122-124	3	17
α-helix	127-152	26

Chain f: 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	20
β-strand	64	1	20
β-strand	75	1	19
β-strand	83-84	2	19
β-strand	94-100	7	20
β-strand	111-116	6	20
β-strand	122-124	3	21
α-helix	127-141	15
α-helix	146-153	8

Chain g: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31-34	4	22
β-strand	41	1	23
β-strand	43-46	4	22
β-strand	53-57	5	20
β-strand	60-65	6	20
β-strand	71	1	22
β-strand	76	1	23
β-strand	82-88	7	20
α-helix	93-96	4
β-strand	97-102	6	20
β-strand	107-109	3	21
α-helix	112-137	26

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
4B1-L	A	protein	244	Homo sapiens
4B1-H	B	protein	248	Homo sapiens
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
TCR-b	n	protein	312	Homo sapiens

Sequence of entity 1 (A), FASTA

>9IRU_1 4B1-L (chains A)
MVSTSQLLGLLLFWTSASRCDIVMTQSPATLSVTPGDRVSLSCRASQSISGYLHWYQQKS
HESPRLLIKYASQSISGIPSRFSGSGSGSDFTLSINSVEPEDVGVYYCQNGHSFPLTFGA
GTKLELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECMKRSPH
PNKG

Sequence of entity 2 (B), FASTA

>9IRU_2 4B1-H (chains B)
MDWTWVFLFLLSVTAGVHSQVQLQQSGAELMKPGASVRISCKATGYTFSRYWIEWVKQRS
GHGLEWIGEILPGSGSTNYNEKFKGKATFTADTSSNTAYMQFSSLTSEDSAVYYCARCYR
YDAYGMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSW
NSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
SCDKTHTC

Sequence of entity 3 (a, b), FASTA

>9IRU_3 T-cell surface glycoprotein CD3 zeta chain (chains a, b)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRS

Sequence of entity 4 (d), FASTA

>9IRU_4 T-cell surface glycoprotein CD3 delta chain (chains d)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 5 (e, f), FASTA

>9IRU_5 T-cell surface glycoprotein CD3 epsilon chain (chains e, f)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 6 (g), FASTA

>9IRU_6 T-cell surface glycoprotein CD3 gamma chain (chains g)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RN

Sequence of entity 7 (m), FASTA

>9IRU_7 CD3-a (chains m)
MKSLRVLLVILWLQLSWVWSQQKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQY
SRKGPELLMYTYSSGNKEDGRFTAQVDKSSKYISLFIRDSQPSDSATYLCAMSKGYSTLT
FGKGTMLLVSPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTV
LDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTN
LNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Sequence of entity 8 (n), FASTA

>9IRU_8 TCR-b (chains n)
MSISLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGM
GLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASRRRQGASG
EQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWV
NGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSEND
EWTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALV
LMAMVKRKDSRG

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2

Primary citation

Cryo-em structure of TCR-4B1 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

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