6R0E: F11TCR

Structure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT. Determined by X-ray diffraction at 1.91 Å resolution. Released 15 Jul 2020.

Method: X-ray diffraction
Resolution: 1.91 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 5
Atoms: 6,958
Mol. weight: 95.33 kDa
Released: 15 Jul 2020

Explore 6R0E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R0E contains 31 α-helices and 75 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 AAA: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	1
β-strand	19-26	8	1
β-strand	29-35	7	1
β-strand	40-43	4	1
α-helix	46-50	5
β-strand	53	1	2
α-helix	57-76	20
α-helix	80-84	5
β-strand	85	1	3
α-helix	86-87	2
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	126-128	3	5
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	161-166	6	5
β-strand	174-178	5	5

Chain BBB: 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	46-49	4	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	136-138	3	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-163	9	7
β-strand	171-176	6	8
β-strand	184-188	5	8

Chain CCC: 1 helix, 1 β-strand

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

Chain DDD: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	9
β-strand	9-13	5	10
α-helix	17	1
β-strand	18-20	3	9
β-strand	22-25	4	9
α-helix	29-30	2
β-strand	31-37	7	10
β-strand	44-49	6	10
β-strand	55-57	3	9
α-helix	59-61	3
β-strand	63-67	5	9
α-helix	68-70	3
β-strand	72-77	6	9
α-helix	82-84	3
β-strand	86-93	8	10
α-helix	99	1
β-strand	100-101	2	10
β-strand	105-110	6	10
α-helix	111	1
β-strand	119-124	6	11
β-strand	125	1	12
β-strand	132-137	6	11
α-helix	145-148	4
β-strand	153-155	3	11
α-helix	156-158	3
β-strand	159-163	5	11
α-helix	164-166	3
β-strand	168-177	10	11
α-helix	184-187	4
β-strand	198	1	11

Chain EEE: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	13
β-strand	8-12	5	14
β-strand	17-22	6	13
β-strand	29-36	8	14
β-strand	40-47	8	14
β-strand	54-55	2	14
β-strand	62-65	4	13
β-strand	71-76	6	13
α-helix	81-83	3
β-strand	85-92	8	14
β-strand	98-100	3	14
β-strand	104-109	6	14
α-helix	112-114	3
β-strand	116	1	15
α-helix	117-118	2
β-strand	119-123	5	12
α-helix	124-126	3
α-helix	127-133	7
β-strand	135-145	11	12
β-strand	146	1	15
β-strand	150-156	7	16
β-strand	159-161	3	16
β-strand	165-167	3	12
α-helix	171	1
β-strand	172-173	2	12
β-strand	183-192	10	12
α-helix	193-196	4
β-strand	202-209	8	16
β-strand	212	1	17
α-helix	223-224	2
β-strand	226	1	17
β-strand	228-235	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	AAA	protein	183	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-1 beta chain	BBB	protein	191	Homo sapiens	P01911 (AlphaFold model)
Hemagglutinin	CCC	protein	13	Influenza A virus	P03435
F11-TCR Alpha Chain	DDD	protein	202	Homo sapiens
F11-TCR Beta Chain	EEE	protein	240	Homo sapiens

Sequence of entity 1 (AAA), FASTA

>6R0E_1 HLA class II histocompatibility antigen, DR alpha chain (chains AAA)
MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGA
LANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNV
TWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWE
FDA

Sequence of entity 2 (BBB), FASTA

>6R0E_2 HLA class II histocompatibility antigen, DRB1-1 beta chain (chains BBB)
MGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAE
YWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSV
SGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPS
VTSPLTVEWRA

Sequence of entity 3 (CCC), FASTA

>6R0E_3 Hemagglutinin (chains CCC)
PKYVKQNTLKLAT

Sequence of entity 4 (DDD), FASTA

>6R0E_4 F11-TCR Alpha Chain (chains DDD)
AQSVTQLGSHVSVSEGALVLLRCNYSSSVPPYLFWYVQYPNQGLQLLLKYTSAATLVKGI
NGFEAEFKKSETSFHLTKPSAHMSDAAEYFCAVSEQDDKIIFGKGTRLHILPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPS

Sequence of entity 5 (EEE), FASTA

>6R0E_5 F11-TCR Beta Chain (chains EEE)
ADVTQTPRNRITKTGKRIMLECSQTKGHDRMYWYRQDPGLGLRLIYYSFDVKDINKGEIS
DGYSVSRQAQAKFSLSLESAIPNQTALYFCATSDESYGYTFGSGTRLTVVEDLNKVSPPE
VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN
DSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD

Primary citation

CD4+T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features. Greenshields-Watson, A., Attaf, M., MacLachlan, B.J. et al. Cell Rep (2020) 32:107885-107885. DOI 10.1016/j.celrep.2020.107885 · 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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