8PJG: F11 TCR

F11 TCR in complex with Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A virus haemagglutinin (HA)306-318 PKYVKQNTLKLAR. Determined by X-ray diffraction at 1.83 Å resolution. Released 19 Jun 2024.

Method: X-ray diffraction
Resolution: 1.83 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 5
Atoms: 7,240
Mol. weight: 96.61 kDa
Ligands: P4G
Released: 19 Jun 2024

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

Secondary structure: helices and β-sheets

8PJG contains 28 α-helices and 74 β-strands across 5 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: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-51	6
β-strand	53	1	2
α-helix	57-76	20
α-helix	80-84	5
β-strand	85	1	3
β-strand	88-93	6	4
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	5
β-strand	126-127	2	5
β-strand	133-134	2	4
α-helix	137	1
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
β-strand	174-179	6	5

Chain B: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	47-49	3	1
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	6
α-helix	96-97	2
β-strand	98-103	6	7
β-strand	113-122	10	7
β-strand	123	1	6
β-strand	128-133	6	8
β-strand	136-137	2	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2
α-helix	5-12	8

Chain D: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	10-14	5	10
α-helix	18	1
β-strand	19-21	3	9
β-strand	23-26	4	9
α-helix	30-31	2
β-strand	32-38	7	10
β-strand	44-50	7	10
β-strand	56-58	3	9
α-helix	60-62	3
β-strand	64-68	5	9
α-helix	69-71	3
β-strand	73-78	6	9
α-helix	83-85	3
β-strand	87-94	8	10
β-strand	101-102	2	10
β-strand	106-111	6	10
β-strand	120-126	7	11
β-strand	133-138	6	11
α-helix	146-149	4
β-strand	154-156	3	11
α-helix	157-159	3
β-strand	160-164	5	11
β-strand	169-178	10	11
α-helix	185-188	4
β-strand	199	1	11

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
β-strand	9-13	5	13
β-strand	18-24	7	12
β-strand	30-37	8	13
β-strand	41-48	8	13
β-strand	55-56	2	13
β-strand	63-69	7	12
β-strand	72-77	6	12
α-helix	82-84	3
β-strand	86-93	8	13
β-strand	99-101	3	13
β-strand	105-110	6	13
α-helix	113-115	3
β-strand	117	1	14
α-helix	118-119	2
β-strand	120-125	6	11
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	11
β-strand	147	1	14
β-strand	151-157	7	15
β-strand	160-162	3	15
β-strand	166-168	3	11
α-helix	172	1
β-strand	173-174	2	11
β-strand	184-193	10	11
α-helix	194-197	4
β-strand	203-210	8	15
β-strand	213	1	16
α-helix	224-225	2
β-strand	227	1	16
β-strand	229-236	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	183	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1 beta chain	B	protein	191	Homo sapiens	P01911 (AlphaFold model)
Hemagglutinin HA2 chain	C	protein	13	Influenza A virus	P03437
T cell receptor alpha chain constant	D	protein	207	Homo sapiens
T cell receptor beta constant 1	E	protein	241	Homo sapiens

Sequence of entity 1 (A), FASTA

>8PJG_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGA
LANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNV
TWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWE
FDA

Sequence of entity 2 (B), FASTA

>8PJG_2 HLA class II histocompatibility antigen, DRB1 beta chain (chains B)
MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAE
YWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSV
SGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPS
VTSPLTVEWRA

Sequence of entity 3 (C), FASTA

>8PJG_3 Hemagglutinin HA2 chain (chains C)
PKYVKQNTLKLAR

Sequence of entity 4 (D), FASTA

>8PJG_4 T cell receptor alpha chain constant (chains D)
MAQSVTQLGSHVSVSEGALVLLRCNYSSSVPPYLFWYVQYPNQGLQLLLKYTSAATLVKG
INGFEAEFKKSETSFHLTKPSAHMSDAAEYFCAVSEQDDKIIFGKGTRLHILPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>8PJG_5 T cell receptor beta constant 1 (chains E)
MADVTQTPRNRITKTGKRIMLECSQTKGHDRMYWYRQDPGLGLRLIYYSFDVKDINKGEI
SDGYSVSRQAQAKFSLSLESAIPNQTALYFCATSDESYGYTFGSGTRLTVVEDLNKVSPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Ligands and cofactors

ID	Name	Formula	Copies
P4G	1-ethoxy-2-(2-ethoxyethoxy)ethane	C8 H18 O3	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

A targeted single mutation in influenza A virus universal epitope transforms immunogenicity and protective immunity via CD4 + T cell activation. Hulin-Curtis, S., Geary, J.K., MacLachlan, B.J. et al. Cell Rep (2024) 43:114259-114259. DOI 10.1016/j.celrep.2024.114259 · PubMed

Other PDB entries of the same protein (UniProt P01903 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5NI9 1.33 Å, Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340
4X5W 1.34 Å, HLA-DR1 with CLIP102-120(M107W)
5NIG 1.35 Å, Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340…
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
8PJF 1.48 Å, Human Leukocyte Antigen class II allotype DR1 presenting P11T->R modified influenza A…
6QZC 1.64 Å, HLA-DR1 with the QAR Peptide
8CMG 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 nsp14 peptide…
8CMH 1.64 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike…
4MD5 1.65 Å, Immune Receptor
4MDJ 1.7 Å, Immune Receptor
8PJE 1.7 Å, Human Leukocyte Antigen class II allotype DR1 presenting influenza A virus…
7YX9 1.76 Å, MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

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