9BBC: TCR GDN detergent micelle

TCR GDN detergent micelle. Determined by electron microscopy at 3.3 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,440
Mol. weight: 186.44 kDa
Ligands: NAG, CLR
Released: 2 Oct 2024

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

Secondary structure: helices and β-sheets

9BBC contains 28 α-helices and 79 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: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
β-strand	29-33	5	2
β-strand	38-44	7	1
β-strand	49	1	3
β-strand	53-57	5	2
β-strand	64-65	2	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	106-110	5	2
β-strand	113	1	3
β-strand	127-132	6	2
β-strand	141-145	5	4
α-helix	146-148	3
β-strand	154-159	6	4
β-strand	175-177	3	4
α-helix	178-180	3
β-strand	181-185	5	4
β-strand	190-199	10	4
α-helix	206-209	4
β-strand	220	1	4
α-helix	230-234	5
α-helix	241-272	32

Chain B: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	5
β-strand	29-33	5	6
β-strand	38-40	3	7
β-strand	41-44	4	5
β-strand	50-57	8	6
β-strand	61-68	8	6
β-strand	75	1	6
β-strand	84-85	2	7
β-strand	89	1	5
β-strand	92	1	5
β-strand	95-97	3	7
α-helix	102-104	3
β-strand	106-113	8	6
β-strand	122-123	2	6
β-strand	127-132	6	6
α-helix	135-137	3
β-strand	139	1	8
β-strand	142-146	5	9
α-helix	147-149	3
α-helix	150-155	6
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
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
β-strand	249	1	11
β-strand	251-258	8	10
α-helix	267-304	38

Chain D: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	12
β-strand	32-36	5	12
β-strand	42-46	5	13
β-strand	50-51	2	12
β-strand	57-62	6	12
α-helix	63-65	3
β-strand	68-72	5	13
β-strand	85-91	7	13
β-strand	96-98	3	14
α-helix	101-125	25

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	65	1	13
β-strand	75-77	3	15
β-strand	81-84	4	15
α-helix	89-92	4
β-strand	94-98	5	13
β-strand	110-116	7	13
β-strand	122-124	3	14
α-helix	127-148	22

Chain F: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
β-strand	37-41	5	16
β-strand	44-48	5	16
β-strand	57-61	5	17
β-strand	64-66	3	17
β-strand	75-77	3	16
β-strand	81-84	4	16
α-helix	89-92	4
β-strand	94-100	7	17
α-helix	105-107	3
β-strand	111-116	6	17
β-strand	124	1	18
α-helix	127-150	24

Chain G: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	31-34	4	19
β-strand	41-46	6	19
β-strand	53-57	5	17
β-strand	60-65	6	17
β-strand	71-76	6	19
α-helix	77-79	3
β-strand	83-88	6	17
β-strand	97-102	6	17
β-strand	107	1	18
α-helix	112-136	25

Chain X: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	29-32	4
α-helix	37-46	10
α-helix	47-50	4

Chain Y: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-54	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCRa	A	protein	273	Homo sapiens	P01848 (AlphaFold model)
TCRb	B	protein	305	Homo sapiens	P01850 (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	137	Homo sapiens	P09693
T-cell surface glycoprotein CD3 zeta chain	X, Y	protein	164	Homo sapiens	P20963

Sequence of entity 1 (A), FASTA

>9BBC_1 TCRa (chains A)
METLLGLLILWLQLQWVSSKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPG
KGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVRPLYGGSYI
PTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDK
TVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETD
TNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWS

Sequence of entity 2 (B), FASTA

>9BBC_2 TCRb (chains B)
MSIGLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGM
GLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGE
LFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVN
GKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDE
WTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVL
MAMVK

Sequence of entity 3 (D), FASTA

>9BBC_3 T-cell surface glycoprotein CD3 delta chain (chains D)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 4 (E, F), FASTA

>9BBC_4 T-cell surface glycoprotein CD3 epsilon chain (chains E, F)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 5 (G), FASTA

>9BBC_5 T-cell surface glycoprotein CD3 gamma chain (chains G)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIA

Sequence of entity 6 (X, Y), FASTA

>9BBC_6 T-cell surface glycoprotein CD3 zeta chain (chains X, Y)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
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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