9CTU: SARS-CoV-2 M (short conformation)bound to C1P

Cryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P. Determined by electron microscopy at 3.03 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.03 Å
Organisms: Mus musculus, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 9,714
Mol. weight: 161.7 kDa
Ligands: 1PX
Released: 6 Nov 2024

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

Secondary structure: helices and β-sheets

9CTU contains 28 α-helices and 105 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.

Chain A: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	19-36	18
α-helix	44-70	27
α-helix	75-106	32
α-helix	109-112	4
β-strand	119-123	5	24
β-strand	128-132	5	24
β-strand	139-145	7	24
β-strand	148-151	4	24
β-strand	154-158	5	24
β-strand	167-172	6	24
β-strand	175-186	12	24
β-strand	192-201	10	24

Chain B: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	17-36	20
α-helix	44-70	27
α-helix	75-106	32
α-helix	109-112	4
β-strand	119-123	5	25
β-strand	128-132	5	25
β-strand	139-145	7	25
β-strand	148-151	4	25
β-strand	154-158	5	25
β-strand	167-172	6	25
β-strand	175-181	7	25
β-strand	185-186	2	25
β-strand	192-201	10	25

Chain C: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	30-31	2	3
β-strand	34-35	2	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
α-helix	116-117	2
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	149-154	6	6
β-strand	157-159	3	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	195-201	7	6
β-strand	209-214	6	6

Chain D: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
β-strand	34-40	7	9
β-strand	44-51	8	9
β-strand	58-60	3	9
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-97	6	9
β-strand	103	1	9
β-strand	107-108	2	9
β-strand	109-111	3	8
α-helix	114-116	3
β-strand	117	1	10
β-strand	120-124	5	11
β-strand	136-145	10	11
β-strand	146	1	10
β-strand	151-154	4	12
β-strand	163-171	9	11
β-strand	174-183	10	11
β-strand	194-199	6	12
β-strand	204-209	6	12

Chain E: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	31	1	15
β-strand	34	1	15
β-strand	37-42	6	14
β-strand	49-53	5	14
β-strand	57-58	2	14
α-helix	59	1
β-strand	66-69	4	13
β-strand	74-79	6	13
α-helix	84-86	3
β-strand	89-94	6	14
α-helix	101	1
β-strand	102	1	14
α-helix	103	1
β-strand	106-111	6	14
β-strand	115	1	16
α-helix	116-117	2
β-strand	118-122	5	17
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	17
β-strand	144	1	16
β-strand	149-154	6	18
β-strand	157-159	3	18
β-strand	163-167	5	17
α-helix	168-171	4
β-strand	177-186	10	17
α-helix	187-190	4
β-strand	195-201	7	18
β-strand	209-214	6	18

Chain F: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	10-12	3	20
β-strand	18-25	8	19
β-strand	34-40	7	20
β-strand	44-51	8	20
β-strand	58-60	3	20
β-strand	65	1	19
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-97	6	20
β-strand	103	1	20
β-strand	107-111	5	20
α-helix	114-116	3
β-strand	117	1	21
β-strand	120-124	5	22
β-strand	136-145	10	22
β-strand	146	1	21
β-strand	151-154	4	23
β-strand	163-171	9	22
β-strand	174-183	10	22
β-strand	194-199	6	23
β-strand	204-209	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
short conformation Fab light chain	C, E	protein	238	Mus musculus
short conformation Fab heavy chain	D, F	protein	255	Mus musculus
Membrane protein	A, B	protein	231	Severe acute respiratory syndrome coronavirus 2	P0DTC5 (AlphaFold model)

Sequence of entity 1 (C, E), FASTA

>9CTU_1 short conformation Fab light chain (chains C, E)
MVLQTQVFISLLLWISGAYGDIVMTQSPASLAVSLGQRATISCKASQSIDYDGDNYMNWY
QQKPGQPPKLLIYTTSNLESGIPARFSGSGSGTDFTLNIHPVEEGDAATYYCQQNNEDPY
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (D, F), FASTA

>9CTU_2 short conformation Fab heavy chain (chains D, F)
MKHLWFFLLLVAAPRWVLSEVQLQQSGPELVKPGASMKISCKTSGYSFTGYTMNWVKQSH
GKNLEWIGLINPYNGDTSYNQKFKGKATLTVDKSSSTAYMELLSLTSEDSAVYYCEVINT
YWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSS
GVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCI
CTVPEVSSHHHHHHH

Sequence of entity 3 (A, B), FASTA

>9CTU_3 Membrane protein (chains A, B)
MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPV
TLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILL
NVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYK
LGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQSNSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
1PX	(2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate	C34 H68 N O6 P	2

Water and common crystallization additives (K) are not listed.

Primary citation

Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly. Dutta, M., Dolan, K.A., Amiar, S. et al. bioRxiv (2024). DOI 10.1101/2024.11.04.620124 · 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
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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