8EUQ: HLA-DRA01:01/HLA-DRB104:01

Crystal structure of HLA-DRA*01:01/HLA-DRB1*04:01 in complex with c44H10 Fab. Determined by X-ray diffraction at 3.09 Å resolution. Released 19 Apr 2023.

Method: X-ray diffraction
Resolution: 3.09 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 8
Atoms: 13,053
Mol. weight: 192.81 kDa
Ligands: NAG
Released: 19 Apr 2023

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

Secondary structure: helices and β-sheets

8EUQ contains 47 α-helices and 156 β-strands across 8 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: 3 helices, 17 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	57-75	19
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	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
β-strand	182	1	5

Chain B: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	2
α-helix	9-14	6
β-strand	36-47	12	1
β-strand	52-61	10	1
β-strand	64-70	7	1
β-strand	76-78	3	1
α-helix	81-83	3
α-helix	84-92	9
α-helix	94-103	10
α-helix	104-109	6
α-helix	110-115	6
β-strand	124	1	23
β-strand	127-133	7	24
β-strand	143-151	9	24
β-strand	152	1	23
β-strand	157-162	6	25
β-strand	166	1	25
β-strand	171-173	3	24
β-strand	177-178	2	24
β-strand	184-190	7	24
β-strand	199-205	7	25
β-strand	213-218	6	25

Chain C: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	11-12	2	27
β-strand	18-25	8	26
β-strand	32-39	8	8
β-strand	46-51	6	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	26
β-strand	77-82	6	26
α-helix	84-86	3
β-strand	88-96	9	8
β-strand	100D-103	4	8
β-strand	107-109	3	8
β-strand	110-111	2	27
α-helix	115-116	2
β-strand	117	1	28
β-strand	120-124	5	29
α-helix	131-134	4
β-strand	137-145	9	29
β-strand	146	1	28
β-strand	151-154	4	30
β-strand	163-165	3	29
α-helix	166-168	3
β-strand	169-170	2	29
β-strand	176-183	8	29
α-helix	186-190	5
β-strand	195-200	6	30
α-helix	201-203	3
β-strand	205-210	6	30

Chain D: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	12-13	2	7
β-strand	19-25	7	6
β-strand	33-38	6	8
β-strand	44-49	6	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	64-67	4	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	103	1	8
β-strand	105-106	2	7
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	154	1	11
β-strand	159-160	2	10
β-strand	163	1	10
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	192-197	6	11
β-strand	205-209	5	11

Chain F: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-15	11	12
β-strand	19-26	8	12
β-strand	29-35	7	12
β-strand	40-43	4	12
α-helix	46-50	5
β-strand	53	1	13
α-helix	56-76	21
α-helix	80-83	4
β-strand	85	1	14
α-helix	86-87	2
β-strand	88-93	6	15
β-strand	103-112	10	15
β-strand	113	1	14
β-strand	118-123	6	16
β-strand	126-128	3	16
β-strand	133-134	2	15
β-strand	138-139	2	15
β-strand	145-153	9	15
β-strand	160-166	7	16
α-helix	173	1
β-strand	174-179	6	16

Chain G: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	13
α-helix	9-16	8
β-strand	36-47	12	12
β-strand	52-61	10	12
β-strand	64-70	7	12
β-strand	75-78	4	12
α-helix	81-83	3
α-helix	84-92	9
α-helix	94-101	8
α-helix	103	1
α-helix	104-109	6
α-helix	110-114	5
β-strand	124	1	31
β-strand	127-133	7	32
β-strand	143-151	9	32
β-strand	152	1	31
β-strand	157-162	6	33
β-strand	165-166	2	33
β-strand	171-173	3	32
β-strand	177-178	2	32
β-strand	184-190	7	32
β-strand	199-205	7	33
β-strand	213-218	6	33

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	17
β-strand	12-13	2	18
β-strand	19-25	7	17
β-strand	33-38	6	19
β-strand	44-49	6	19
β-strand	53-54	2	19
α-helix	55	1
β-strand	64-67	4	17
β-strand	70-75	6	17
α-helix	80-82	3
β-strand	85-90	6	19
α-helix	96	1
β-strand	97-98	2	19
β-strand	103	1	19
β-strand	105-106	2	18
β-strand	111	1	20
α-helix	112-113	2
β-strand	114-118	5	21
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	154	1	22
β-strand	159-160	2	21
β-strand	163	1	21
β-strand	173-182	10	21
α-helix	183-186	4
β-strand	191-197	7	22
β-strand	205-210	6	22

Chain I: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	34
β-strand	11-12	2	35
β-strand	18-25	8	34
β-strand	32-39	8	19
β-strand	46-51	6	19
β-strand	57-59	3	19
β-strand	67-72	6	34
β-strand	77-82	6	34
α-helix	84-86	3
β-strand	88-96	9	19
β-strand	103	1	19
β-strand	107-109	3	19
β-strand	110-111	2	35
α-helix	115-116	2
β-strand	117	1	36
β-strand	120-124	5	37
β-strand	132	1	37
β-strand	135-145	11	37
β-strand	146	1	36
β-strand	151-154	4	38
β-strand	163-165	3	37
α-helix	166-168	3
β-strand	169-170	2	37
β-strand	176-185	10	37
α-helix	186-189	4
β-strand	195-200	6	38
α-helix	201-203	3
β-strand	205-210	6	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, F	protein	188	Homo sapiens	P01903 (AlphaFold model)
c44H10 Fab light chain	D, H	protein	214	Homo sapiens
Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain	B, G	protein	226	Influenza A virus, Homo sapiens	A0A1V1IGJ9 (AlphaFold model), P04664
c44H10 Fab heavy chain	C, I	protein	223	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>8EUQ_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, F)
EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALAN
IAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWL
RNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDT
SGENLYFQ

Sequence of entity 2 (D, H), FASTA

>8EUQ_2 c44H10 Fab light chain (chains D, H)
DIQMTQSPSSLSASLGQRVSLTCRASQEISGYLTWLQQKPDGTIKRLVYAASTLDSGVPK
RFSGSRSGSDYSLTISSLESEDFADYYCLQYTNYPLTFGAGTKLELKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B, G), FASTA

>8EUQ_3 Hemagglutinin HA1 chain,HLA class II histocompatibility antigen DR beta chain (chains B, G)
GAPKYVKQNTLKLATSGGSGSIEGRGSGDTRPRFLEQVKHECHFFNGTERVRFLDRYFYH
QEEYVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQR
RVYPEVTVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDW
TFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRATGGENLYFQ

Sequence of entity 4 (C, I), FASTA

>8EUQ_4 c44H10 Fab heavy chain (chains C, I)
QVQLKESGPGLVAPSQSLSITCTVSGFSLTSYGVHWVRQPPGKGLEWLGVIWAGGSINYN
SALMSRLSISKDNFKSQVFLKMSSLQTDDTAMYYCARAYGDYVHYAMDYWGQGTSVTASS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Ligands and cofactors

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

Water and common crystallization additives (SO4) are not listed.

Primary citation

Modular adjuvant-free pan-HLA-DR-immunotargeting subunit vaccine against SARS-CoV-2 elicits broad sarbecovirus-neutralizing antibody responses. Kassardjian, A., Sun, E., Sookhoo, J. et al. Cell Rep (2023) 42:112391-112391. DOI 10.1016/j.celrep.2023.112391 · 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

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8EUQ: HLA-DRA*01:01/HLA-DRB1*04:01