6M1V: Post fusion core of 2019-nCoV S2 subunit

Crystal structure of post fusion core of 2019-nCoV S2 subunit. Determined by X-ray diffraction at 1.5 Å resolution. Released 3 Jun 2020.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 1
Atoms: 823
Mol. weight: 12.69 kDa
Released: 3 Jun 2020

Explore 6M1V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M1V contains 4 α-helices and 0 β-strands across 1 chain. 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, 0 β-strands

Element	Residues	Length
α-helix	919-967	49
α-helix	1180-1192	13
α-helix	1193-1196	4
α-helix	1200-1202	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S2,Spike protein S2	A	protein	119	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6M1V_1 Spike protein S2,Spike protein S2 (chains A)
MENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLLVPRGSGGSG
GSGGLEVLFQGPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELHHHHHH

Primary citation

Structural basis of HCoV-19 fusion core and an effective inhibition peptide against virus entry. Sun, H., Li, Y., Liu, P. et al. Emerg Microbes Infect (2020) 9:1238-1241. DOI 10.1080/22221751.2020.1770631 · PubMed

Other PDB entries of the same protein (UniProt P0DTC2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z8O 0.96 Å, Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide
7Y8J 1.03 Å, 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2
9FC2 1.21 Å, The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the…
7EK6 1.24 Å, Structure of viral peptides IPB19/N52
7EAM 1.4 Å, immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6
7M53 1.4 Å, B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide
8CMC 1.42 Å, Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530
7M8U 1.45 Å, Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from…
7ZR2 1.45 Å, Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
8D36 1.45 Å, Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody…
8ENS 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail…
8ENW 1.45 Å, Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike…

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