9CQ4: OKT3 Fab heavy chain

G115 gamma delta TCR/CD3 complex bound by OKT3 Fab. Determined by electron microscopy at 3.27 Å resolution. Released 15 Jan 2025.

Method: Electron microscopy
Resolution: 3.27 Å
Organisms: Mus musculus, Homo sapiens
Chains: 12
Atoms: 8,397
Mol. weight: 290.25 kDa
Ligands: NAG, CLR
Released: 15 Jan 2025

Explore 9CQ4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CQ4 contains 17 α-helices and 86 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	224-256	33

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	248-284	37

Chains C and H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	9-12	4	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	93-100	8	2
β-strand	105-109	5	2
β-strand	110	1	1
β-strand	113-117	5	2

Chain D: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	3
β-strand	10-13	4	4
β-strand	18-25	8	3
β-strand	33-37	5	4
β-strand	44-48	5	4
β-strand	52-53	2	4
β-strand	61-66	6	3
β-strand	69-75	7	3
β-strand	84-88	5	4
β-strand	89	1	5
β-strand	96	1	5
β-strand	101-105	5	4

Chain E: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	37-40	4	14
β-strand	44-48	5	14
β-strand	57-61	5	12
β-strand	65-66	2	12
β-strand	76-77	2	14
β-strand	82-85	4	14
β-strand	94-100	7	12
β-strand	110-114	5	12
β-strand	122-124	3	13
α-helix	127-154	28

Chain F: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	39-40	2	15
β-strand	44-48	5	15
β-strand	57-61	5	16
β-strand	65-66	2	16
β-strand	75-77	3	15
β-strand	81-85	5	15
β-strand	95	1	17
β-strand	96-100	5	16
α-helix	105-107	3
β-strand	111-116	6	17
β-strand	122	1	18
α-helix	127-155	29

Chain G: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	19
β-strand	41-43	3	20
β-strand	44-46	3	19
β-strand	54-57	4	17
β-strand	60-63	4	17
β-strand	73-76	4	20
α-helix	77-79	3
β-strand	83-88	6	17
β-strand	93	1	17
β-strand	97-102	6	17
β-strand	109	1	18
α-helix	112-135	24

Chain K: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	11
β-strand	33-35	3	11
β-strand	41-46	6	12
β-strand	50	1	11
α-helix	55-57	3
β-strand	59-61	3	11
α-helix	63-65	3
β-strand	68-73	6	12
β-strand	84-89	6	12
β-strand	96-98	3	13
α-helix	103-126	24

3 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
OKT3 Fab heavy chain	C, H	protein	238	Mus musculus
OKT3 Fab light chain	D, L	protein	213	Mus musculus
G115 TCR delta chain	A	protein	283	Homo sapiens
G115 TCR gamma chain	B	protein	295	Homo sapiens
T-cell surface glycoprotein CD3 delta chain	K	protein	174	Homo sapiens	P04234 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	E, F	protein	210	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 gamma chain	G	protein	185	Homo sapiens	P09693 (AlphaFold model)
T-cell surface glycoprotein CD3 zeta chain	Y, Z	protein	173	Homo sapiens	P20963 (AlphaFold model)

Sequence of entity 1 (C, H), FASTA

>9CQ4_1 OKT3 Fab heavy chain (chains C, H)
QVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPGQGLEWIGYINPSRGYTNY
NQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLG

Sequence of entity 2 (D, L), FASTA

>9CQ4_2 OKT3 Fab light chain (chains D, L)
QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAH
FRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A), FASTA

>9CQ4_3 G115 TCR delta chain (chains A)
AIELVPEHQTVPVSIGVPATLRCSMKGEAIGNYYINWYRKTQGNTMTFIYREKDIYGPGF
KDNFQGDIDIAKNLAVLKILAPSERDEGSYYCACDTLGMGGEYTDKLIFGKGTRVTVEPR
SQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKL
GKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETENTKQPSKSCHKPKAIVHTE
KVNMMSLTVLGLRMLFAKTVAVNFLLTAKLFFLSRGRAKRGSG

Sequence of entity 4 (B), FASTA

>9CQ4_4 G115 TCR gamma chain (chains B)
AGHLEQPQISSTKTLSKTARLECVVSGITISATSVYWYRERPGEVIQFLVSISYDGTVRK
ESGIPSGKFEVDRIPETSTSTLTIHNVEKQDIATYYCALWEAQQELGKKIKVFGPGTKLI
ITDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILGSQ
EGNTMKTNDTYMKFSWLTVPEKSLDKEHRCIVRHENNKNGVDQEIIFPPIKTDVITMDPK
DNCSKDANDTLLLQLTNTSAYYMYLLLLLKSVVYFAIITCCLLRRTAFCCNGEKS

Sequence of entity 5 (K), FASTA

>9CQ4_5 T-cell surface glycoprotein CD3 delta chain (chains K)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNKGSG

Sequence of entity 6 (E, F), FASTA

>9CQ4_6 T-cell surface glycoprotein CD3 epsilon chain (chains E, F)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRIGSG

Sequence of entity 7 (G), FASTA

>9CQ4_7 T-cell surface glycoprotein CD3 gamma chain (chains G)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RNGSG

Sequence of entity 8 (Y, Z), FASTA

>9CQ4_8 T-cell surface glycoprotein CD3 zeta chain (chains Y, Z)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRGSGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structural characterization of two gamma delta TCR/CD3 complexes. Hoque, M., Grigg, J.B., Ramlall, T. et al. Nat Commun (2025) 16:318-318. DOI 10.1038/s41467-024-55467-5 · PubMed

Other PDB entries of the same protein (UniProt P04234 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1XIW 1.9 Å, Crystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody…
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
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
9IRU 3.14 Å, Cryo-em structure of TCR-4B1 complex
9IRS 3.18 Å, Cryo-EM structure of the TCR-OKT3 complex
7FJD 3.2 Å, Cryo-EM structure of a membrane protein(WT)

Browse structure collections

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