8CMI: PDB entry 8CMI

Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S761-775. Determined by X-ray diffraction at 2.6 Å resolution. Released 26 Jul 2023.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 9
Atoms: 9,714
Mol. weight: 137.89 kDa
Released: 26 Jul 2023

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

Secondary structure: helices and β-sheets

8CMI contains 46 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: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	1-4	4
β-strand	5-15	11	1
β-strand	19-26	8	1
β-strand	29-35	7	1
α-helix	37-39	3
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
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	137	1
β-strand	138-139	2	4
β-strand	145-153	9	4
β-strand	160-166	7	5
α-helix	173	1
β-strand	174-179	6	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	46-49	4	1
α-helix	52-54	3
α-helix	55-62	8
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	98-104	7	7
β-strand	114-122	9	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	155-162	8	7
β-strand	170-176	7	8
β-strand	184-189	6	8

Chain C: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	2
α-helix	3-8	6
α-helix	10-12	3

Chain D: 6 helices, 18 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	98	1	13
β-strand	101	1	13
β-strand	103-112	10	12
β-strand	113	1	11
β-strand	118-123	6	14
β-strand	126-128	3	14
β-strand	133-134	2	12
α-helix	137	1
β-strand	138-139	2	12
β-strand	145-153	9	12
β-strand	161-166	6	14
α-helix	173	1
β-strand	174-178	5	14

Chain E: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	9
β-strand	23-32	10	9
β-strand	36-41	6	9
β-strand	46-49	4	9
α-helix	52-54	3
α-helix	55-62	8
α-helix	65-74	10
α-helix	75-80	6
α-helix	81-86	6
α-helix	87-89	3
β-strand	95	1	15
α-helix	96-97	2
β-strand	98-103	6	16
β-strand	114-122	9	16
β-strand	123	1	15
β-strand	128-133	6	17
β-strand	136-137	2	17
β-strand	142-144	3	16
β-strand	148-149	2	16
β-strand	155-162	8	16
α-helix	165-166	2
β-strand	170-176	7	17
β-strand	184-189	6	17

Chain F: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	10
α-helix	4	1
α-helix	9-12	4

Chain G: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	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	80-84	5
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
α-helix	173	1
β-strand	174-179	6	22

Chain H: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	7-18	12	18
β-strand	23-32	10	18
β-strand	36-41	6	18
β-strand	47-49	3	18
α-helix	55-62	8
α-helix	65-74	10
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
α-helix	104-105	2
β-strand	114-122	9	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	155-162	8	24
α-helix	165-166	2
β-strand	170-176	7	25
β-strand	184-189	6	25

1 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, 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

>8CMI_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

>8CMI_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

>8CMI_3 Spike protein S2' (chains C, F, I)
TQLKRALTGIAVEQD

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

Browse structure collections

About this viewer

MolViewer shows 8CMI 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.