8CMD: PDB entry 8CMD

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S761-775. Determined by X-ray diffraction at 2.54 Å resolution. Released 26 Jul 2023.

Method: X-ray diffraction
Resolution: 2.54 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 9
Atoms: 9,751
Mol. weight: 136.83 kDa
Released: 26 Jul 2023

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

Secondary structure: helices and β-sheets

8CMD contains 39 α-helices and 98 β-strands across 9 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	52-53	2	2
α-helix	56-76	21
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	126-127	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	161-166	6	5
β-strand	174-178	5	5

Chain B: 6 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	65-74	10
α-helix	75-80	6
α-helix	81-86	6
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	170-176	7	8
β-strand	184-189	6	8

Chains C and F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	2
α-helix	4-5	2
α-helix	9-12	4

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	9
β-strand	19-26	8	9
β-strand	29-35	7	9
β-strand	40-43	4	9
α-helix	46-50	5
β-strand	52-53	2	10
α-helix	56-76	21
α-helix	80-84	5
β-strand	85	1	11
α-helix	86-87	2
β-strand	88-93	6	12
β-strand	103-112	10	12
β-strand	113	1	11
β-strand	118-123	6	13
β-strand	126-128	3	13
β-strand	133-134	2	12
α-helix	137	1
β-strand	138-139	2	12
β-strand	145-153	9	12
β-strand	160-166	7	13
β-strand	174-179	6	13

Chain E: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	9
β-strand	23-32	10	9
β-strand	35-41	7	9
β-strand	47-49	3	9
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
β-strand	95	1	14
α-helix	96-97	2
β-strand	98-103	6	15
β-strand	113-122	10	15
β-strand	123	1	14
β-strand	128-133	6	16
β-strand	136-138	3	16
β-strand	142-144	3	15
β-strand	148-149	2	15
β-strand	155-163	9	15
β-strand	170-176	7	16
β-strand	184-189	6	16

Chain G: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	17
β-strand	19-26	8	17
β-strand	29-35	7	17
β-strand	40-43	4	17
α-helix	46-50	5
β-strand	52-53	2	18
α-helix	57-76	20
α-helix	80-84	5
β-strand	85	1	19
α-helix	86-87	2
β-strand	88-93	6	20
β-strand	98	1	21
β-strand	101	1	21
β-strand	103-112	10	20
β-strand	113	1	19
β-strand	118-123	6	22
β-strand	126-128	3	22
β-strand	133-134	2	20
α-helix	137	1
β-strand	138-139	2	20
β-strand	145-153	9	20
β-strand	161-166	6	22
β-strand	174-178	5	22

Chain H: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	17
β-strand	23-32	10	17
β-strand	35-41	7	17
β-strand	47-49	3	17
α-helix	52-54	3
α-helix	55-63	9
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	23
α-helix	96-97	2
β-strand	98-103	6	24
β-strand	113-122	10	24
β-strand	123	1	23
β-strand	128-133	6	25
β-strand	136-138	3	25
β-strand	142-144	3	24
β-strand	148-149	2	24
β-strand	155-163	9	24
β-strand	170-176	7	25
β-strand	184-189	6	25

Chain I: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	18
α-helix	4-5	2
α-helix	9-14	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class II histocompatibility antigen, DR alpha chain	A, D, G	protein	183	Homo sapiens	P01903 (AlphaFold model)
Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101)	B, E, H	protein	194	Homo sapiens	D7RIG0 (AlphaFold model)
Spike protein S2'	C, F, I	protein	15	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>8CMD_1 HLA class II histocompatibility antigen, DR alpha chain (chains A, D, G)
MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGA
LANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNV
TWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWE
FDA

Sequence of entity 2 (B, E, H), FASTA

>8CMD_2 Human leukocyte antigen DR beta chain allotype DR1 (DRB1*0101) (chains B, E, H)
MGSMGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRP
DAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLV
CSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVE
HPSVTSPLTVEWRA

Sequence of entity 3 (C, F, I), FASTA

>8CMD_3 Spike protein S2' (chains C, F, I)
TQLNRALTGIAVEQD

Primary citation

Structural definition of HLA class II-presented SARS-CoV-2 epitopes reveals a mechanism to escape pre-existing CD4 + T cell immunity. Chen, Y., Mason, G.H., Scourfield, D.O. et al. Cell Rep (2023) 42:112827-112827. DOI 10.1016/j.celrep.2023.112827 · 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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