7VGR: SARS-CoV-2 M protein dimer

SARS-CoV-2 M protein dimer (long form) in complex with YN7756_1 Fab. Determined by electron microscopy at 2.7 Å resolution. Released 3 Aug 2022.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Mus musculus, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 9,872
Mol. weight: 154.79 kDa
Released: 3 Aug 2022

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

Secondary structure: helices and β-sheets

7VGR contains 28 α-helices and 118 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-36	26
α-helix	44-70	27
α-helix	77-105	29
α-helix	109-112	4
β-strand	118-123	6	31
β-strand	128-133	6	31
β-strand	139-140	2	31
β-strand	149-151	3	32
β-strand	154-157	4	32
β-strand	167-170	4	31
β-strand	177-182	6	31
β-strand	186	1	33
β-strand	192	1	33
β-strand	195-200	6	31

Chains C and E: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	1
β-strand	10-14	5	2
β-strand	19-24	6	1
β-strand	31	1	3
β-strand	34	1	3
β-strand	37-42	6	2
β-strand	49-53	5	2
β-strand	57-58	2	2
α-helix	59	1
β-strand	66-69	4	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	89-94	6	2
β-strand	102	1	2
β-strand	106-111	6	2
β-strand	115	1	4
β-strand	118-122	5	5
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	5
β-strand	144	1	4
β-strand	148-154	7	6
β-strand	157-158	2	6
β-strand	163-167	5	5
α-helix	168-171	4
β-strand	177-186	10	5
α-helix	187-190	4
β-strand	195-202	8	6
β-strand	205-214	10	6

Chains D and F: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	37-39	3	9
β-strand	45-46	2	9
β-strand	49-52	4	10
β-strand	57-60	4	10
β-strand	65	1	7
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	93-95	3	9
β-strand	98	1	11
β-strand	109	1	11
β-strand	114-115	2	9
β-strand	116-118	3	8
α-helix	121-123	3
β-strand	124	1	12
β-strand	127-131	5	13
β-strand	142-152	11	13
β-strand	153	1	12
β-strand	158-161	4	14
α-helix	162-164	3
β-strand	170-178	9	13
β-strand	181-191	11	13
β-strand	201	1	15
β-strand	202-206	5	14
β-strand	211-213	3	14
β-strand	216	1	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
YN7756_1 Fab light chain	C, E	protein	218	Mus musculus
YN7756_1 Fab heavy chain	D, F	protein	236	Mus musculus
Membrane protein	A, B	protein	246	Severe acute respiratory syndrome coronavirus 2	P0DTC5 (AlphaFold model)

Sequence of entity 1 (C, E), FASTA

>7VGR_1 YN7756_1 Fab light chain (chains C, E)
DIVLTQSPASLTVSLGQRATISCRASESVDSFGNSFMHWYQQKPGQPPKLLIYRASNLES
GIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSSEDPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (D, F), FASTA

>7VGR_2 YN7756_1 Fab heavy chain (chains D, F)
EVQLQQSGAELVRPGSSVKISCKGSGYVFSNYWMNWVKQRPGQGLEWIGQIYPGDGDTNY
NGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCASGYLGENYVMDFWGQGTSVTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVPEVSS

Sequence of entity 3 (A, B), FASTA

>7VGR_3 Membrane protein (chains A, B)
MHHHHHHHHDYKDDDDKENLYFQGMADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQ
FAYANRNRFLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYF
IASFRLFARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHL
GRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDN
IALLVQ

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…
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
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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