7PHR: T-cell receptor alpha chain

Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I. Determined by electron microscopy at 3.08 Å resolution. Released 31 Aug 2022.

Method: Electron microscopy
Resolution: 3.08 Å
Organisms: Homo sapiens, Aequorea victoria
Chains: 11
Atoms: 11,511
Mol. weight: 202.5 kDa
Ligands: NAG
Released: 31 Aug 2022

Explore 7PHR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PHR contains 45 α-helices and 109 β-strands across 11 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: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
β-strand	20-25	6	2
β-strand	32-38	7	1
β-strand	44-51	8	1
β-strand	56-59	4	2
β-strand	62-67	6	2
β-strand	72-77	6	2
α-helix	82-84	3
β-strand	86-92	7	1
β-strand	99	1	1
β-strand	104-109	6	1
β-strand	118-121	4	3
α-helix	122	1
β-strand	123	1	4
α-helix	124-125	2
β-strand	131-138	8	3
α-helix	145-147	3
β-strand	153-154	2	3
α-helix	155-157	3
β-strand	158-162	5	3
β-strand	167-176	10	3
α-helix	186-188	3
β-strand	197	1	3
α-helix	207-210	4
α-helix	211-213	3
α-helix	218-249	32

Chain B: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	5
β-strand	11-15	5	6
β-strand	20-22	3	7
β-strand	23-26	4	5
β-strand	32-39	8	6
β-strand	43-50	8	6
β-strand	57-58	2	6
β-strand	65-67	3	7
β-strand	74	1	5
β-strand	77-79	3	7
β-strand	88-95	8	6
β-strand	103-104	2	6
β-strand	108-113	6	6
α-helix	116-118	3
β-strand	120	1	8
α-helix	121-122	2
β-strand	123-127	5	9
β-strand	128	1	4
α-helix	129-130	2
α-helix	131-136	6
β-strand	139-149	11	9
β-strand	150	1	8
β-strand	154-160	7	10
β-strand	163-165	3	10
β-strand	169-171	3	9
β-strand	187-196	10	9
α-helix	197-200	4
β-strand	206-213	8	10
β-strand	216	1	11
α-helix	227-228	2
β-strand	230	1	11
β-strand	232-239	8	10
α-helix	248-285	38

Chain C: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	12
β-strand	19-24	6	12
β-strand	31-35	5	13
β-strand	38-43	6	13
β-strand	50-54	5	12
α-helix	55-57	3
β-strand	61	1	14
β-strand	63-66	4	13
α-helix	71-73	3
β-strand	75-79	5	14
β-strand	85-87	3	15
α-helix	90-115	26

Chain D: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-8	4	16
β-strand	11-15	5	16
β-strand	21-25	5	17
β-strand	29-30	2	16
β-strand	36-41	6	16
β-strand	48-53	6	17
α-helix	58-60	3
β-strand	62-70	9	17
β-strand	75-77	3	18
α-helix	80-106	27

Chain e: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	17-19	3	27
β-strand	22-26	5	27
β-strand	35-39	5	14
β-strand	43-44	2	14
β-strand	53-56	4	27
β-strand	59-62	4	27
β-strand	72-78	7	14
α-helix	83-85	3
β-strand	89-93	5	14
β-strand	100-102	3	15
α-helix	105-133	29

Chain E: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
β-strand	15-19	5	19
β-strand	22-26	5	19
β-strand	35-39	5	17
β-strand	42-44	3	17
β-strand	53-56	4	19
β-strand	59-62	4	19
β-strand	72-78	7	17
α-helix	83-85	3
β-strand	89-94	6	17
β-strand	100-102	3	18
α-helix	105-131	27

Chain H: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	20
β-strand	21-28	8	20
β-strand	31-37	7	20
β-strand	46-47	2	20
α-helix	57-84	28
β-strand	94-103	10	20
β-strand	109-118	10	20
β-strand	121-126	6	20
β-strand	133-135	3	20
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	21
α-helix	184-185	2
β-strand	186	1	22
β-strand	189-192	4	22
β-strand	198-208	11	22
β-strand	209	1	21
β-strand	214-219	6	23
β-strand	222-223	2	23
β-strand	228-230	3	22
α-helix	231-233	3
β-strand	234-235	2	22
β-strand	241-250	10	22
α-helix	254-256	3
β-strand	257-262	6	23
β-strand	270-272	3	23

Chain L: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	24
α-helix	4-5	2
β-strand	6-11	6	25
α-helix	14-15	2
β-strand	21-30	10	25
β-strand	31	1	24
β-strand	36-41	6	26
β-strand	44-45	2	26
β-strand	50-51	2	25
β-strand	55-56	2	25
β-strand	62-70	9	25
α-helix	76-77	2
β-strand	78-83	6	26
β-strand	91-94	4	26
α-helix	95	1

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
T-cell receptor alpha chain	A	protein	251	Homo sapiens
T-cell receptor beta chain	B	protein	290	Homo sapiens
T-cell surface glycoprotein CD3 gamma chain	C	protein	122	Homo sapiens	P09693 (AlphaFold model)
T-cell surface glycoprotein CD3 delta chain, green fluorescent protein	D	protein	356	Homo sapiens, Aequorea victoria	P04234 (AlphaFold model), P42212 (AlphaFold model)
T-cell surface glycoprotein CD3 epsilon chain	E, e	protein	136	Homo sapiens	P07766 (AlphaFold model)
HLA class I histocompatibility antigen, A alpha chain	H	protein	304	Homo sapiens	P04439
Beta-2-microglobulin	L	protein	101	Homo sapiens	P61769
Tumor-associated antigentic peptide gp100	P	protein	9	Homo sapiens	P40967
T-cell surface glycoprotein CD3 zeta chain	Z, z	protein	36	Homo sapiens	P20963

Sequence of entity 1 (A), FASTA

>7PHR_1 T-cell receptor alpha chain (chains A)
MSQQGEEDPQALSIQEGENATMNCSYKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSG
RLRVTLDTSKKSSSLLITASRAADTASYFCATDGSTPMQFGKGTRLSVIPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAGF
NLLMTLRLWSS

Sequence of entity 2 (B), FASTA

>7PHR_2 T-cell receptor beta chain (chains B)
MDGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSWAQGDFQKGD
IAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSWGAPYEQYFGPGTRLTVTEDLNKVF
PPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQP
ALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RADCGFTSVSYQQGVLSATILYEILLGKATLYAVLVSALVLMAMVKRKDF

Sequence of entity 3 (C), FASTA

>7PHR_3 T-cell surface glycoprotein CD3 gamma chain (chains C)
QSIKGNHLVKVYDYQEDGSVLLTCDAEAKNITWFKDGKMIGFLTEDKKKWNLGSNAKDPR
GMYQCKGSQNKSKPLQVYYRMCQNCIELNAATISGFLFAEIVSIFVLAVGVYFIAGQDGV
RQ

Sequence of entity 4 (D), FASTA

>7PHR_4 T-cell surface glycoprotein CD3 delta chain, green fluorescent protein (chains D)
FKIPIEELEDRVFVNCNTSITWVEGTVGTLLSDITRLDLGKRILDPRGIYRCNGTDIYKD
KESTVQVHYRMCQSCVELDPATVAGIIVTDVIATLLLALGVFCFAGHETGRDPPVATMVS
KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVT
TLSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNR
IELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHY
QQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYK

Sequence of entity 5 (E, e), FASTA

>7PHR_5 T-cell surface glycoprotein CD3 epsilon chain (chains E, e)
DGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIGGDEDDKNIGSDEDHL
SLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATIVIVDICITG
GLLLLVYYWSKNRKAK

Sequence of entity 6 (H), FASTA

>7PHR_6 HLA class I histocompatibility antigen, A alpha chain (chains H)
MGSSHHHHHHGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPR
APWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWR
FLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWL
RRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDT
ELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSSQPEDQVDPRL
IDGK

Sequence of entity 7 (L), FASTA

>7PHR_7 Beta-2-microglobulin (chains L)
MGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSK
DWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 8 (P), FASTA

>7PHR_8 Tumor-associated antigentic peptide gp100 (chains P)
YLEPGPVTV

Sequence of entity 9 (Z, z), FASTA

>7PHR_9 T-cell surface glycoprotein CD3 zeta chain (chains Z, z)
QSFGLLDPKLCYLLDGILFIYGVILTALFLRVKFSR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Susac, L., Vuong, M.T., Thomas, C. et al. Cell (2022) 185:3201-3213.e19. DOI 10.1016/j.cell.2022.07.010 · PubMed

Other PDB entries of the same protein (UniProt P09693 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Q5U 2.4 Å, The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide
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
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)
9JY2 3.24 Å, Fab-CD3-delta epsilon-TCR complex

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