8TW4: TCR in nanodisc ND-I

TCR in nanodisc ND-I. Determined by electron microscopy at 3.3 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Escherichia coli str. K-12 substr. MG1655, human respiratory syncytial virus
Chains: 8
Atoms: 6,401
Mol. weight: 275.5 kDa
Ligands: NAG, CLR
Released: 2 Oct 2024

Explore 8TW4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TW4 contains 23 α-helices and 77 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	1
β-strand	38-40	3	2
β-strand	53-55	3	3
β-strand	65-68	4	3
β-strand	75	1	4
β-strand	78	1	5
β-strand	81	1	5
β-strand	82	1	2
β-strand	84	1	4
β-strand	94-96	3	2
α-helix	101-103	3
β-strand	106-107	2	6
β-strand	108-109	2	3
β-strand	127-128	2	6
β-strand	130-131	2	1
β-strand	141-144	4	7
β-strand	146	1	8
α-helix	147-148	2
β-strand	154-159	6	7
α-helix	163-165	3
β-strand	175-177	3	7
β-strand	183	1	9
α-helix	186-188	3
β-strand	192	1	9
β-strand	194-199	6	7
α-helix	206-209	4
β-strand	220	1	7
α-helix	246-252	7
α-helix	254-266	13

Chain B: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	10
β-strand	33	1	11
β-strand	39-40	2	12
β-strand	41-43	3	10
β-strand	50-57	8	13
β-strand	61-65	5	13
β-strand	95-96	2	12
β-strand	107-113	7	13
β-strand	122	1	13
β-strand	128	1	13
β-strand	132	1	11
α-helix	140-141	2
β-strand	142-145	4	14
β-strand	147	1	8
α-helix	150-156	7
β-strand	160-166	7	14
β-strand	176-177	2	15
β-strand	178-179	2	16
β-strand	182-183	2	16
β-strand	188	1	14
β-strand	195-196	2	14
β-strand	206-213	8	14
β-strand	228-232	5	15
β-strand	235	1	17
α-helix	247-248	2
β-strand	249	1	17
β-strand	251-255	5	15
α-helix	277-286	10
α-helix	289-297	9
α-helix	300-303	4

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	42-43	2	23
β-strand	50-51	2	24
β-strand	58-59	2	24
β-strand	71-72	2	23
β-strand	75	1	25
β-strand	84	1	25
β-strand	87	1	23
α-helix	89-90	2
α-helix	102-113	12

Chain E: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	37-41	5	18
β-strand	44-48	5	18
β-strand	58-61	4	19
β-strand	65-66	2	19
β-strand	75-77	3	18
β-strand	81-85	5	18
β-strand	94-99	6	19
β-strand	112-114	3	19
α-helix	127-129	3
α-helix	130-134	5
α-helix	136-143	8

Chain F: 0 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	37-38	2	20
β-strand	44-48	5	20
β-strand	57-59	3	21
β-strand	76-77	2	20
β-strand	81-85	5	20
β-strand	95-96	2	22
β-strand	98-100	3	21
β-strand	112-114	3	22

Chain G: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	26
β-strand	41-44	4	27
β-strand	46	1	26
β-strand	53-57	5	22
β-strand	60-65	6	22
β-strand	72-76	5	27
β-strand	83-88	6	22
β-strand	97-100	4	22
α-helix	112-126	15

Chain X: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	33-35	3
α-helix	38-40	3
α-helix	41-47	7

Chain Y: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	33-45	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR alpha	A	protein	274	Homo sapiens	P01848 (AlphaFold model)
T cell receptor beta variable 6-5, T cell receptor beta chain MC.7.G5, MCHERRY fusion protein	B	protein	556	Homo sapiens, Escherichia coli str. K-12 substr. MG1655	A0A0K0K1A5 (AlphaFold model), P0DTU4 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	E, F	protein	207	Homo sapiens	P07766 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain	D	protein	171	Homo sapiens	P04234
T-cell surface glycoprotein CD3 gamma chain	G	protein	190	Homo sapiens	P09693
T-cell surface glycoprotein CD3 zeta chain,RNA-directed RNA polymerase L	X, Y	protein	412	Homo sapiens, human respiratory syncytial virus	A0A5P9VSM8, P20963

Sequence of entity 1 (A), FASTA

>8TW4_1 TCR alpha (chains A)
METLLGLLILWLQLQWVSSKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPG
KGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVRPLYGGSYI
PTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDK
TVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETD
TNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Sequence of entity 2 (B), FASTA

>8TW4_2 T cell receptor beta variable 6-5, T cell receptor beta chain MC.7.G5, MCHERRY fusion protein (chains B)
MSIGLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGM
GLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGE
LFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVN
GKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDE
WTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVL
MAMVKRKDSRGASLEVLFQGPVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEG
RPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWER
VMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDG
ALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYE
RAEGRHSTGGMDELYK

Sequence of entity 3 (E, F), FASTA

>8TW4_3 T-cell surface glycoprotein CD3 epsilon chain (chains E, F)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 4 (D), FASTA

>8TW4_4 T-cell surface glycoprotein CD3 delta chain (chains D)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 5 (G), FASTA

>8TW4_5 T-cell surface glycoprotein CD3 gamma chain (chains G)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RNHHHHHHHH

Sequence of entity 6 (X, Y), FASTA

>8TW4_6 T-cell surface glycoprotein CD3 zeta chain,RNA-directed RNA polymerase L (chains X, Y)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRASLEVLFQGPVSKGEE
LFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTY
GVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELK
GIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNT
PIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
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. bioRxiv (2024). DOI 10.1101/2023.08.22.554360 · 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

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