8TRL: PDB entry 8TRL

T cell recognition of citrullinated alpha-enolase peptide presented by HLA-DR4. Determined by X-ray diffraction at 2.4 Å resolution. Released 31 Jul 2024.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,917
Mol. weight: 195.61 kDa
Ligands: NAG
Released: 31 Jul 2024

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

Secondary structure: helices and β-sheets

8TRL contains 54 α-helices and 146 β-strands across 10 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	46-50	5
β-strand	53	1	2
α-helix	56-76	21
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: 8 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	65-72	8
α-helix	74	1
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	115-122	8	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	155-161	7	7
β-strand	171-176	6	8
β-strand	184-188	5	8

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	11	1	2

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	18
β-strand	19-26	8	18
β-strand	29-35	7	18
β-strand	40-43	4	18
α-helix	46-50	5
β-strand	53	1	19
α-helix	56-76	21
α-helix	81-84	4
β-strand	85	1	20
α-helix	86-87	2
β-strand	88-93	6	21
β-strand	103-112	10	21
β-strand	113	1	20
β-strand	118-123	6	22
β-strand	126-128	3	22
β-strand	133-134	2	21
α-helix	137	1
β-strand	138-139	2	21
β-strand	145-153	9	21
β-strand	160-166	7	22
β-strand	174-179	6	22

Chain E: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	18
β-strand	23-32	10	18
β-strand	35-41	7	18
β-strand	46-49	4	18
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-72	8
α-helix	74	1
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	23
α-helix	96-97	2
β-strand	98-103	6	24
β-strand	115-122	8	24
β-strand	123	1	23
β-strand	128-133	6	25
β-strand	136-137	2	25
β-strand	142-144	3	24
β-strand	148-149	2	24
β-strand	155-161	7	24
α-helix	169-170	2
β-strand	171-176	6	25
β-strand	184-187	4	25

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	11	1	19
α-helix	18-21	4

Chain G: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	26
β-strand	10-14	5	27
α-helix	18	1
β-strand	19-24	6	26
β-strand	37-44	8	27
β-strand	51-56	6	27
β-strand	66-67	2	26
β-strand	77-80	4	26
β-strand	86-91	6	26
α-helix	96-98	3
β-strand	100-108	9	27
β-strand	121-126	6	27
α-helix	127	1
β-strand	135-140	6	28
β-strand	141	1	29
β-strand	148-153	6	28
α-helix	162-164	3
β-strand	170-171	2	28
β-strand	175-179	5	28
β-strand	184-193	10	28
α-helix	200-203	4
β-strand	214	1	28

Chain H: 11 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	30
β-strand	10-14	5	31
β-strand	19-24	6	30
β-strand	38-44	7	31
β-strand	51-57	7	31
β-strand	64-68	5	31
α-helix	72-75	4
β-strand	76-79	4	30
β-strand	87-91	5	30
α-helix	96-98	3
β-strand	100-107	8	31
α-helix	114-115	2
β-strand	116-117	2	31
β-strand	121-126	6	31
α-helix	129-131	3
β-strand	133	1	32
α-helix	134-135	2
β-strand	136-140	5	29
α-helix	141-143	3
α-helix	144-150	7
β-strand	152-162	11	29
β-strand	163	1	32
β-strand	167-173	7	33
β-strand	176-178	3	33
β-strand	182-184	3	29
α-helix	188	1
β-strand	189-190	2	29
α-helix	198-199	2
β-strand	200-209	10	29
α-helix	210-214	5
β-strand	219-226	8	33
β-strand	229	1	34
α-helix	240-241	2
β-strand	243	1	34
β-strand	245-252	8	33

2 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
HLA class II histocompatibility antigen, DR alpha chain	A, D	protein	181	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1 beta chain	B, E	protein	190	Homo sapiens	P01911 (AlphaFold model)
Alpha-enolase	C, F	protein	13	Homo sapiens	P06733 (AlphaFold model)
RA2.7 TCR alpha chain	G, I	protein	204	Homo sapiens
RA2.7 TCR beta chain	H, J	protein	245	Homo sapiens

Sequence of entity 1 (A, D), FASTA

>8TRL_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
D

Sequence of entity 2 (B, E), FASTA

>8TRL_2 HLA class II histocompatibility antigen, DRB1 beta chain (chains B, E)
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVN
GFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSL
TSPLTVEWRA

Sequence of entity 3 (C, F), FASTA

>8TRL_3 Alpha-enolase (chains C, F)
EIFDSRGNPTGEV

Sequence of entity 4 (G, I), FASTA

>8TRL_4 RA2.7 TCR alpha chain (chains G, I)
MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMAS
LIITEDRKSSTLILPHATLRDTAVYYCIVNPANTGNQFYFGTGTSLTVIPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (H, J), FASTA

>8TRL_5 RA2.7 TCR beta chain (chains H, J)
MEPEVTQTPSHQVTQMGQEVILRCVPISNHLYFYWYRQILGQKVEFLVSFYNNEISEKSE
IFDDQFSVERPDGSNFTLKIRSTKLEDSAMYFCASRRDYFSYEQYFGPGTRLTVTEDLNK
VFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Water and common crystallization additives (ACT, GOL, FMT) are not listed.

Primary citation

The molecular basis underlying T cell specificity towards citrullinated epitopes presented by HLA-DR4. Loh, T.J., Lim, J.J., Jones, C.M. et al. Nat Commun (2024) 15:6201-6201. DOI 10.1038/s41467-024-50511-w · 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

Browse structure collections

About this viewer

MolViewer shows 8TRL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.