6V19: Immune receptor complex

immune receptor complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 6,521
Mol. weight: 97.82 kDa
Ligands: NAG
Released: 25 Nov 2020

Explore 6V19 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V19 contains 26 α-helices and 81 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, 18 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	48-50	3
β-strand	53	1	2
α-helix	57-76	20
α-helix	80-82	3
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-93	6	4
β-strand	98	1	5
β-strand	101	1	5
β-strand	103-112	10	4
β-strand	113	1	3
β-strand	118-123	6	6
β-strand	126-127	2	6
β-strand	133-134	2	4
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	6
β-strand	174-179	6	6

Chain B: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	1
β-strand	23-32	10	1
β-strand	36-41	6	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	75-79	5
α-helix	80-85	6
β-strand	95	1	7
β-strand	98-103	6	8
β-strand	115-120	6	8
β-strand	122	1	9
β-strand	123	1	7
β-strand	128-130	3	10
β-strand	142-144	3	8
β-strand	148-149	2	9
β-strand	155-156	2	9
β-strand	158-161	4	8
β-strand	172-176	5	10
β-strand	184-187	4	10

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	70	1	2
α-helix	75-80	6

Chain D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
β-strand	9-14	6	12
β-strand	19-21	3	13
β-strand	23-26	4	11
β-strand	33-44	8	12
β-strand	51-56	6	12
β-strand	66-69	4	13
β-strand	79-82	4	13
β-strand	86	1	11
β-strand	89-91	3	13
α-helix	96-98	3
β-strand	100-108	9	12
β-strand	112	1	14
α-helix	115	1
β-strand	116-117	2	12
α-helix	118	1
β-strand	121-126	6	12
α-helix	127-128	2
β-strand	135-140	6	15
β-strand	141	1	16
β-strand	148-153	6	15
α-helix	161-163	3
β-strand	169-171	3	15
α-helix	172-174	3
β-strand	175-179	5	15
β-strand	184-193	10	15
α-helix	200-202	3
β-strand	214	1	15

Chain E: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	10-14	5	18
β-strand	19-25	7	17
β-strand	31-44	7	18
β-strand	50-57	8	18
β-strand	60-68	5	18
β-strand	76-79	4	17
β-strand	86-91	6	17
α-helix	96-98	3
β-strand	100-107	8	18
β-strand	111	1	14
α-helix	115-116	2
β-strand	117-118	2	18
β-strand	122-127	6	18
α-helix	130-132	3
β-strand	134	1	19
α-helix	135-136	2
β-strand	137-141	5	16
α-helix	142-144	3
α-helix	145-151	7
β-strand	153-163	11	16
β-strand	164	1	19
β-strand	168-174	7	20
β-strand	177-179	3	20
β-strand	183-185	3	16
β-strand	190-191	2	16
β-strand	201-210	10	16
α-helix	211-214	4
β-strand	220-227	8	20
β-strand	230	1	21
α-helix	241-242	2
β-strand	244	1	21
β-strand	246-253	8	20

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 72,74cit69-81	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

>6V19_1 HLA class II histocompatibility antigen, DR alpha chain (chains A)
IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGAL
ANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVT
WLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF
DTSGDDDDK

Sequence of entity 2 (B), FASTA

>6V19_2 HLA class II histocompatibility antigen, DRB1-4 beta chain (chains B)
GDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEY
WNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVN
GFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSL
TSPLTVEWRATGGDDDDK

Sequence of entity 3 (C), FASTA

>6V19_3 Fibrinogen beta 72,74cit69-81 (chains C)
GGYRARPAKAAAT

Sequence of entity 4 (D), FASTA

>6V19_4 M134 TCR alpha chain (chains D)
GDSVTQTEGQVTVSESKSLIINCTYSATSIAYPNLFWYVRYPGEGLQLLLKVITAGQKGS
SRGFEATYNKETTSFHLQKASVQESDSAVYYCALSDSSSFSKLVFGQGTSLSVVPNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6V19_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	1

Water and common crystallization additives (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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