9CTW: Long conformation Fab light chain

Cryo-EM structure of SARS-CoV-2 M (long conformation) in the presence of C1P. Determined by electron microscopy at 3.01 Å resolution. Released 6 Nov 2024.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Mus musculus, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 9,754
Mol. weight: 161.66 kDa
Released: 6 Nov 2024

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

Secondary structure: helices and β-sheets

9CTW contains 32 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	18-36	19
α-helix	44-70	27
α-helix	75-106	32
α-helix	109-112	4
β-strand	118-124	7	29
β-strand	127-133	7	29
β-strand	139-143	5	29
β-strand	149-151	3	29
β-strand	154-157	4	29
β-strand	167-171	5	29
β-strand	176-187	12	29
β-strand	191-200	10	29

Chains C and E: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
β-strand	10-14	5	2
β-strand	19-23	5	1
β-strand	37-42	6	2
β-strand	49-53	5	2
β-strand	57-58	2	2
α-helix	59	1
β-strand	66-71	6	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	89-94	6	2
β-strand	101-102	2	2
β-strand	106-111	6	2
β-strand	115	1	3
β-strand	118-122	5	4
α-helix	123-125	3
α-helix	126-131	6
β-strand	133-143	11	4
β-strand	144	1	3
β-strand	148-154	7	5
β-strand	157-158	2	5
β-strand	163-167	5	4
α-helix	169-171	3
β-strand	177-186	10	4
α-helix	187-192	6
β-strand	195-202	8	5
α-helix	208	1
β-strand	209-214	6	5

Chain D: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34	1	8
β-strand	37-39	3	9
β-strand	45-47	3	9
β-strand	49-52	4	8
β-strand	57-60	4	8
β-strand	65	1	6
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	93-94	2	9
β-strand	97-98	2	10
β-strand	109-110	2	10
β-strand	114-115	2	9
β-strand	116-118	3	7
α-helix	121-123	3
β-strand	124	1	11
β-strand	127-131	5	12
β-strand	142-152	11	12
β-strand	153	1	11
β-strand	158-161	4	13
α-helix	162-164	3
β-strand	170-172	3	12
α-helix	173-175	3
β-strand	182-191	10	12
β-strand	201	1	14
β-strand	202-206	5	13
β-strand	211-213	3	13
β-strand	216	1	14

Chain F: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	20
β-strand	10-12	3	21
β-strand	18-25	8	20
α-helix	29-31	3
β-strand	34	1	22
β-strand	37-39	3	21
β-strand	45-47	3	21
β-strand	49-52	4	22
β-strand	57-60	4	22
β-strand	65	1	20
β-strand	68-73	6	20
β-strand	78-83	6	20
α-helix	88-90	3
β-strand	92-94	3	21
β-strand	97-98	2	23
β-strand	109-110	2	23
β-strand	114-118	5	21
α-helix	121-123	3
β-strand	124	1	24
β-strand	127-131	5	25
β-strand	142-152	11	25
β-strand	153	1	24
β-strand	158-161	4	26
α-helix	162-164	3
β-strand	166	1	26
β-strand	171-172	2	25
α-helix	173-175	3
β-strand	178	1	27
β-strand	181	1	27
β-strand	182-191	10	25
β-strand	201	1	28
β-strand	202-206	5	26
β-strand	211-213	3	26
β-strand	216	1	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Long conformation Fab light chain	C, E	protein	238	Mus musculus
Long conformation Fab heavy chain	D, F	protein	262	Mus musculus
Membrane protein	A, B	protein	231	Severe acute respiratory syndrome coronavirus 2	P0DTC5 (AlphaFold model)

Sequence of entity 1 (C, E), FASTA

>9CTW_1 Long conformation Fab light chain (chains C, E)
MVLQTQVFISLLLWISGAYGDIVLTQSPASLTVSLGQRATISCRASESVDSFGNSFMHWY
QQKPGQPPKLLIYRASNLESGIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSSEDPY
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQ
NGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (D, F), FASTA

>9CTW_2 Long conformation Fab heavy chain (chains D, F)
MKHLWFFLLLVAAPRWVLSEVQLQQSGAELVRPGSSVKISCKGSGYVFSNYWMNWVKQRP
GQGLEWIGQIYPGDGDTNYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCASGYL
GENYVMDFWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTW
NSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD
CGCKPCICTVPEVSSHHHHHHH

Sequence of entity 3 (A, B), FASTA

>9CTW_3 Membrane protein (chains A, B)
MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNRFLYIIKLIFLWLLWPV
TLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRLFARTRSMWSFNPETNILL
NVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCDIKDLPKEITVATSRTLSYYK
LGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIALLVQSNSLEVLFQ

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
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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