8TW6: TCR in nanodisc ND-II

TCR in nanodisc ND-II. Determined by electron microscopy at 3.1 Å resolution. Released 2 Oct 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, human respiratory syncytial virus, Escherichia coli str. K-12 substr. MG1655
Chains: 8
Atoms: 6,242
Mol. weight: 274.21 kDa
Ligands: NAG, CLR
Released: 2 Oct 2024

Explore 8TW6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8TW6 contains 19 α-helices and 58 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: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	30-33	4	1
β-strand	40-41	2	2
β-strand	54-58	5	3
β-strand	62-65	4	3
β-strand	78	1	2
β-strand	81-84	4	2
β-strand	93-96	4	2
α-helix	101-103	3
β-strand	106-109	4	3
β-strand	127-128	2	3
β-strand	129-132	4	1
β-strand	141-144	4	4
β-strand	156-159	4	4
β-strand	175-177	3	4
β-strand	181	1	4
β-strand	194-199	6	4
α-helix	201-203	3
α-helix	206-209	4
β-strand	220	1	4
α-helix	246-252	7
α-helix	254-258	5

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	39-43	5	5
β-strand	51-56	6	6
β-strand	63-65	3	6
β-strand	92-96	5	5
β-strand	107-113	7	6
β-strand	121-123	3	6
β-strand	127-128	2	6
α-helix	140-142	3
β-strand	143-146	4	7
α-helix	150-155	6
β-strand	158-165	8	7
β-strand	188-189	2	7
β-strand	209-215	7	7
α-helix	216-219	4
β-strand	227-228	2	8
α-helix	246-247	2
β-strand	255-256	2	8
α-helix	275-294	20

Chain D: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	28-29	2	14
β-strand	32-36	5	14
β-strand	42-43	2	10
β-strand	50-51	2	14
β-strand	57-60	4	14
β-strand	70-74	5	10
β-strand	83-88	6	10
α-helix	101-114	14

Chain E: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	9
β-strand	45-47	3	9
β-strand	58-61	4	10
β-strand	64-65	2	10
β-strand	76	1	9
β-strand	82-83	2	9
β-strand	94-99	6	10
β-strand	110-114	5	10
α-helix	130-142	13

Chain F: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	38-39	2	11
β-strand	46-48	3	11
β-strand	57-59	3	12
β-strand	81-82	2	11
β-strand	98-100	3	12
α-helix	105-107	3
β-strand	111-115	5	13
α-helix	129-145	17

Chain G: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	31-32	2	15
β-strand	43-44	2	16
β-strand	45-46	2	15
β-strand	53-57	5	13
β-strand	60-65	6	13
β-strand	72-73	2	16
β-strand	84-88	5	13
β-strand	97-101	5	13
α-helix	112-127	16

Chain X: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	33-35	3
α-helix	36-40	5
α-helix	41-44	4

Chain Y: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	32-49	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP	X, Y	protein	412	Homo sapiens, human respiratory syncytial virus	A0A5P9VSM6, P20963 (AlphaFold model)
TCR alpha	A	protein	274	Homo sapiens
T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY	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
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

Sequence of entity 1 (X, Y), FASTA

>8TW6_1 T-cell surface glycoprotein CD3 zeta chain, GFP fusion protein,GFP (chains X, Y)
MKWKALFTAAILQAQLPITEAQSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSRSAD
APAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPQRRKNPQEGLYNELQKDKMA
EAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPRASLEVLFQGPVSKGEE
LFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTY
GVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELK
GIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNT
PIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYK

Sequence of entity 2 (A), FASTA

>8TW6_2 TCR alpha (chains A)
METLLGLLILWLQLQWVSSKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPG
KGLTSLLLIQSSQREQTSGRLNASLDKSSGRSTLYIAASQPGDSATYLCAVRPLYGGSYI
PTFGRGTSLIVHPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDK
TVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETD
TNLNFQNLSVIGFRILLLKVAGFNLLMTLRLWSS

Sequence of entity 3 (B), FASTA

>8TW6_3 T cell receptor beta variable 6-5,T cell receptor beta chain MC.7.G5,MCHERRY (chains B)
MSIGLLCCAALSLLWAGPVNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGM
GLRLIHYSVGAGITDQGEVPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYVGNTGE
LFFGEGSRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVN
GKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDE
WTQDRAKPVTQIVSAEAWGRADCGFTSESYQQGVLSATILYEILLGKATLYAVLVSALVL
MAMVKRKDSRGASLEVLFQGPVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEG
RPYEGTQTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWER
VMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDG
ALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYE
RAEGRHSTGGMDELYK

Sequence of entity 4 (E, F), FASTA

>8TW6_4 T-cell surface glycoprotein CD3 epsilon chain (chains E, F)
MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
PPVPNPDYEPIRKGQRDLYSGLNQRRI

Sequence of entity 5 (D), FASTA

>8TW6_5 T-cell surface glycoprotein CD3 delta chain (chains D)
MEHSTFLSGLVLATLLSQVSPFKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDL
GKRILDPRGIYRCNGTDIYKDKESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLAL
GVFCFAGHETGRLSGAADTQALLRNDQVYQPLRDRDDAQYSHLGGNWARNK

Sequence of entity 6 (G), FASTA

>8TW6_6 T-cell surface glycoprotein CD3 gamma chain (chains G)
MEQGKGLAVLILAIILLQGTLAQSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGK
MIGFLTEDKKKWNLGSNAKDPRGMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLF
AEIVSIFVLAVGVYFIAGQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLR
RNHHHHHHHH

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	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

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