9EXA: SARS-CoV-2 M protein dimer

SARS-CoV-2 M protein dimer (short form) in complex with Fab-B and CIM-834. Determined by electron microscopy at 3.2 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Mus musculus
Chains: 6
Atoms: 9,700
Mol. weight: 137.77 kDa
Ligands: A1H7W
Released: 22 Jan 2025

Explore 9EXA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9EXA contains 33 α-helices and 110 β-strands across 6 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.

Chains A and B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	19-38	20
α-helix	44-70	27
α-helix	75-106	32
α-helix	109-112	4
β-strand	118-124	7	1
β-strand	127-132	6	1
β-strand	139-145	7	1
β-strand	148-151	4	1
β-strand	155-158	4	1
β-strand	167-172	6	1
β-strand	175-187	13	1
β-strand	191-202	12	1

Chain C: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	3
β-strand	10-14	5	4
β-strand	19-25	7	3
β-strand	30-31	2	5
β-strand	34-35	2	5
β-strand	37-42	6	4
β-strand	49-53	5	4
β-strand	57-58	2	4
α-helix	59	1
β-strand	66-71	6	3
β-strand	74-79	6	3
α-helix	84-86	3
β-strand	88-94	7	4
α-helix	100	1
β-strand	102	1	4
β-strand	103	1	3
β-strand	106-111	6	4
β-strand	115	1	6
β-strand	120-122	3	7
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	7
β-strand	144	1	6
β-strand	149-154	6	8
β-strand	157-159	3	8
β-strand	163-165	3	7
α-helix	167-171	5
β-strand	177-186	10	7
α-helix	187-191	5
β-strand	195-201	7	8
β-strand	209-214	6	8

Chain D: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
α-helix	7	1
β-strand	10-12	3	10
β-strand	17-25	9	9
α-helix	29-31	3
β-strand	34-40	7	10
β-strand	44-51	8	10
β-strand	58-60	3	10
β-strand	68-73	6	9
β-strand	78-84	7	9
α-helix	88-90	3
β-strand	92-97	6	10
β-strand	107-111	5	10
α-helix	114-116	3
β-strand	117	1	11
β-strand	122-124	3	12
β-strand	135-145	11	12
β-strand	146	1	11
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	159	1	13
β-strand	163-166	4	12
α-helix	167-168	2
β-strand	171	1	14
β-strand	174	1	14
β-strand	175-184	10	12
α-helix	185-187	3
β-strand	194-199	6	13
β-strand	204-209	6	13

Chain E: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-14	5	16
β-strand	19-25	7	15
β-strand	30-31	2	17
β-strand	34-35	2	17
β-strand	37-42	6	16
β-strand	49-53	5	16
β-strand	57-58	2	16
α-helix	59	1
β-strand	66-71	6	15
β-strand	74-79	6	15
β-strand	88-94	7	16
α-helix	100	1
β-strand	102	1	16
β-strand	106-111	6	16
β-strand	115	1	18
β-strand	120-122	3	19
α-helix	123-125	3
α-helix	126-129	4
β-strand	133-143	11	19
β-strand	144	1	18
β-strand	149-154	6	20
β-strand	157-159	3	20
β-strand	163-165	3	19
α-helix	167-171	5
β-strand	177-186	10	19
α-helix	187-191	5
β-strand	196-201	6	20
α-helix	208	1
β-strand	209-213	5	20

Chain F: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	21
β-strand	10-12	3	22
β-strand	18-25	8	21
β-strand	34-40	7	22
β-strand	44-51	8	22
β-strand	58-60	3	22
β-strand	65	1	21
β-strand	68-73	6	21
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-97	6	22
β-strand	107-111	5	22
α-helix	114-116	3
β-strand	117	1	23
β-strand	122-124	3	24
β-strand	137-145	9	24
β-strand	146	1	23
β-strand	151-154	4	25
α-helix	155-157	3
β-strand	159	1	25
β-strand	163-166	4	24
α-helix	167-168	2
β-strand	171	1	26
β-strand	174	1	26
β-strand	175-182	8	24
β-strand	194-198	5	25
β-strand	199	1	27
β-strand	204	1	27
β-strand	207-209	3	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Membrane protein	A, B	protein	188	Severe acute respiratory syndrome coronavirus 2	P0DTC5 (AlphaFold model)
Fab-B light chain	C, E	protein	218	Mus musculus
Fab-B heavy chain	D, F	protein	213	Mus musculus

Sequence of entity 1 (A, B), FASTA

>9EXA_1 Membrane protein (chains A, B)
LEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWI
TGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLES
ELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAY
SRYRIGNY

Sequence of entity 2 (C, E), FASTA

>9EXA_2 Fab-B light chain (chains C, E)
DIVMTQSPASLAVSLGQRATISCKASQSIDYDGDNYMNWYQQKPGQPPKLLIYTTSNLES
GIPARFSGSGSGTDFTLNIHPVEEGDAATYYCQQNNEDPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (D, F), FASTA

>9EXA_3 Fab-B heavy chain (chains D, F)
EVQLQQSGPELVKPGASMKISCKTSGYSFTGYTMNWVKQSHGKNLEWIGLINPYNGDTSY
NQKFKGKATLTVDKSSSTAYMELLSLTSEDSAVYYCEVINTYWGQGTLVTVSAAKTTPPS
VYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

Ligands and cofactors

ID	Name	Formula	Copies
A1H7W	6-[[1-[4,6-dimethyl-5-(2-methylpropyl)pyrimidin-2-yl]piperidin-4-yl]-methyl-ami…	C27 H42 N8 O	2

Primary citation

A coronavirus assembly inhibitor that targets the viral membrane protein. Laporte, M., Jochmans, D., Bardiot, D. et al. Nature (2025) 640:514-523. DOI 10.1038/s41586-025-08773-x · PubMed

Other PDB entries of the same protein (UniProt P0DTC5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8CME 2.26 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Membrane peptide…
7VGR 2.7 Å, SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab
7VGS 2.8 Å, SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab
9CTW 3.01 Å, Cryo-EM structure of SARS-CoV-2 M (long conformation) in the presence of C1P
9CTU 3.03 Å, Cryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P
8W2E 3.06 Å, SARS-CoV-2 M protein dimer in complex with JNJ-9676 and Fab-B
9BF9 3.4 Å, Human LAG-3-HLA-DR1 complex
8CTK 3.52 Å, Cryo-EM structure of SARS-CoV-2 M protein in a lipid nanodisc

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