6V1A: Immune receptor complex

immune receptor complex. Determined by X-ray diffraction at 2.29 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 2.29 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 6,902
Mol. weight: 99.3 kDa
Ligands: NAG
Released: 25 Nov 2020

Explore 6V1A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V1A contains 26 α-helices and 80 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: 5 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	48-51	4
β-strand	53	1	2
α-helix	57-76	20
α-helix	81-84	4
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
α-helix	135-137	3
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	55-63	9
α-helix	67-72	6
α-helix	74	1
α-helix	75-80	6
α-helix	81-85	5
α-helix	87-89	3
β-strand	95	1	6
β-strand	98-101	4	7
β-strand	117-122	6	7
β-strand	123	1	6
β-strand	128-132	5	8
β-strand	137	1	8
β-strand	142-144	3	7
β-strand	148-149	2	7
β-strand	155-161	7	7
β-strand	172-176	5	8
β-strand	184-187	4	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	70	1	2
α-helix	73-80	8

Chain D: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	9
β-strand	10-14	5	10
β-strand	19-21	3	11
β-strand	23-25	3	9
β-strand	33-44	8	10
β-strand	51-56	6	10
β-strand	66-69	4	11
β-strand	79-82	4	11
β-strand	84	1	9
β-strand	86	1	9
β-strand	89-91	3	11
α-helix	96-98	3
β-strand	100-108	9	10
β-strand	116-117	2	10
β-strand	121-126	6	10
α-helix	127-128	2
β-strand	135-141	7	12
β-strand	148-153	6	12
β-strand	160	1	13
α-helix	162-164	3
β-strand	169-171	3	12
α-helix	172-174	3
β-strand	175-179	5	12
β-strand	184-193	10	12
β-strand	208	1	13
β-strand	214	1	12

Chain E: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-14	5	15
β-strand	19-21	3	16
β-strand	22-25	4	14
β-strand	31-44	7	15
β-strand	50-57	8	15
β-strand	60-68	5	15
β-strand	76-79	4	16
β-strand	86	1	14
β-strand	88-91	4	16
α-helix	96-98	3
β-strand	100-107	8	15
α-helix	115-116	2
β-strand	117-118	2	15
β-strand	122-127	6	15
α-helix	130-132	3
β-strand	134	1	17
α-helix	135-136	2
β-strand	137-142	6	12
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	12
β-strand	164	1	17
β-strand	168-174	7	18
β-strand	177-179	3	18
β-strand	183-185	3	12
α-helix	189	1
β-strand	190-191	2	12
β-strand	201-210	10	12
α-helix	211-214	4
β-strand	220-227	8	18
β-strand	230	1	19
α-helix	241-242	2
β-strand	244	1	19
β-strand	246-253	8	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A	protein	189	Homo sapiens	P01903 (AlphaFold model)
HLA class II histocompatibility antigen, DRB1-4 beta chain	B	protein	198	Homo sapiens	P01911 (AlphaFold model)
Fibrinogen beta 74cit69-81	C	protein	13	Homo sapiens	P02675 (AlphaFold model)
M134 TCR alpha chain	D	protein	209	Mus musculus
M134 TCR beta chain	E	protein	242	Mus musculus

Sequence of entity 1 (A), FASTA

>6V1A_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DTSGDDDDK

Sequence of entity 2 (B), FASTA

>6V1A_2 HLA class II histocompatibility antigen, DRB1-4 beta chain (chains B)
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVN
GFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSL
TSPLTVEWRATGGDDDDK

Sequence of entity 3 (C), FASTA

>6V1A_3 Fibrinogen beta 74cit69-81 (chains C)
GGYRARPAKAAAT

Sequence of entity 4 (D), FASTA

>6V1A_4 M134 TCR alpha chain (chains D)
GDSVTQTEGQVTVSESKSLIINCTYSATSIAYPNLFWYVRYPGEGLQLLLKVITAGQKGS
SRGFEATYNKETTSFHLQKASVQESDSAVYYCALSDSSSFSKLVFGQGTSLSVVPNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6V1A_5 M134 TCR beta chain (chains E)
AVFQTPNYHVTQVGNEVSFNCKQTLGHDTMYWYKQDSKKLLKIMFSYNNKQLIVNETVPR
RFSPQSSDKAHLNLRIKSVEPEDSAVYLCASSLDWASQNTLYFGAGTRLSVLEDLNKVFP
PEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

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

Primary citation

The shared susceptibility epitope of HLA-DR4 binds citrullinated self-antigens and the TCR. Lim, J.J., Jones, C.M., Loh, T.J. et al. Sci Immunol (2021) 6. DOI 10.1126/sciimmunol.abe0896 · 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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