7VGS: SARS-CoV-2 M protein dimer

SARS-CoV-2 M protein dimer (short form) in complex with YN7717_9 Fab. Determined by electron microscopy at 2.8 Å resolution. Released 3 Aug 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Severe acute respiratory syndrome coronavirus 2, Mus musculus
Chains: 6
Atoms: 9,700
Mol. weight: 153.51 kDa
Released: 3 Aug 2022

Explore 7VGS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VGS contains 22 α-helices and 114 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: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-36	27
α-helix	46-67	22
α-helix	79-105	27
β-strand	119-122	4	1
β-strand	129-132	4	1
β-strand	139-141	3	1
β-strand	142-143	2	2
β-strand	149-151	3	2
β-strand	154-157	4	2
β-strand	166-170	5	1
β-strand	176-180	5	1
β-strand	186	1	3
β-strand	192	1	3
β-strand	195-201	7	1

Chains C and E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	11-13	3	4
β-strand	19-21	3	5
α-helix	31-33	3
β-strand	38-42	5	6
β-strand	49-52	4	6
β-strand	54	1	7
β-strand	56	1	7
α-helix	58-59	2
β-strand	66-71	6	5
β-strand	74-79	6	5
β-strand	89-93	5	6
β-strand	102	1	6
β-strand	106-107	2	6
β-strand	108-110	3	4
β-strand	115	1	8
α-helix	116-117	2
β-strand	118-122	5	9
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	9
β-strand	144	1	8
β-strand	149-154	6	10
β-strand	157-159	3	10
β-strand	163-167	5	9
α-helix	168-171	4
β-strand	177-186	10	9
α-helix	187-190	4
β-strand	195-201	7	10
β-strand	209-214	6	10

Chains D and F: 1 helix, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
β-strand	10-12	3	12
β-strand	18-21	4	13
β-strand	22-25	4	11
β-strand	35-40	6	14
β-strand	44-51	8	14
β-strand	58-60	3	14
β-strand	65	1	13
β-strand	68-69	2	13
β-strand	72-73	2	15
β-strand	78-79	2	15
β-strand	80-83	4	13
α-helix	88-90	3
β-strand	93-97	5	14
β-strand	107-108	2	14
β-strand	109-111	3	12
β-strand	117	1	16
β-strand	120-124	5	17
β-strand	136-145	10	17
β-strand	146	1	16
β-strand	151-154	4	18
β-strand	163-171	9	17
β-strand	174-183	10	17
β-strand	194-199	6	18
β-strand	204-209	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Membrane protein	A, B	protein	246	Severe acute respiratory syndrome coronavirus 2	P0DTC5 (AlphaFold model)
YN7717_9 Fab light chain	C, E	protein	218	Mus musculus
YN7717_9 Fab heavy chain	D, F	protein	229	Mus musculus

Sequence of entity 1 (A, B), FASTA

>7VGS_1 Membrane protein (chains A, B)
MHHHHHHHHDYKDDDDKENLYFQGMADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQ
FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYF
IASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHL
GRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDN
IALLVQ

Sequence of entity 2 (C, E), FASTA

>7VGS_2 YN7717_9 Fab light chain (chains C, E)
DIVMTQSPASLAVSLGQRATISCKASQSIDYDGDNYMNWYQQKPGQPPKLLIYTTSNLES
GIPARFSGSGSGTDFTLNIHPVEEGDAATYYCQQNNEDPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (D, F), FASTA

>7VGS_3 YN7717_9 Fab heavy chain (chains D, F)
EVQLQQSGPELVKPGASMKISCKTSGYSFTGYTMNWVKQSHGKNLEWIGLINPYNGDTSY
NQKFKGKATLTVDKSSSTAYMELLSLTSEDSAVYYCEVINTYWGQGTLVTVSAAKTTPPS
VYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSS
VTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVPEVSS

Primary citation

Structure of SARS-CoV-2 membrane protein essential for virus assembly. Zhang, Z., Nomura, N., Muramoto, Y. et al. Nat Commun (2022) 13:4399-4399. DOI 10.1038/s41467-022-32019-3 · 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
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
9EXA 3.2 Å, SARS-CoV-2 M protein dimer (short form) in complex with Fab-B and CIM-834
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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