5OMI: Pre-glycoprotein polyprotein GP complex

Crystal structure of GP2 from Lassa virus in a post fusion conformation. Determined by X-ray diffraction at 2.56 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 2.56 Å
Organism: Lassa mammarenavirus
Chains: 3
Atoms: 2,714
Mol. weight: 41.95 kDa
Ligands: NAG
Released: 29 Aug 2018

Explore 5OMI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OMI contains 23 α-helices and 6 β-strands across 3 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: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	306-354	49
α-helix	356-358	3
α-helix	361-362	2
β-strand	363	1	1
α-helix	364	1
α-helix	368-373	6
β-strand	386	1	1
α-helix	390-392	3
α-helix	393-397	5
α-helix	402-417	16

Chain B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	306-354	49
α-helix	356-358	3
α-helix	361-362	2
β-strand	363	1	2
α-helix	364	1
α-helix	368-376	9
β-strand	386	1	2
α-helix	390-392	3
α-helix	393-397	5
α-helix	402-416	15

Chain C: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	306-354	49
α-helix	361-362	2
β-strand	363	1	3
α-helix	364	1
α-helix	368-377	10
β-strand	386	1	3
α-helix	390-392	3
α-helix	393-397	5
α-helix	402-415	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pre-glycoprotein polyprotein GP complex	A, B, C	protein	118	Lassa mammarenavirus	P08669 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>5OMI_1 Pre-glycoprotein polyprotein GP complex (chains A, B, C)
GGSGDEEFSDMLRLFDFNKQAIQRLKAEAQMSIQLINKAVNALINDQLIMKNHLRDIMGI
PYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEY

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Water and common crystallization additives (NA, CL) are not listed.

Primary citation

Variations in Core Packing of GP2 from Old World Mammarenaviruses in their Post-Fusion Conformations Affect Membrane-Fusion Efficiencies. Shulman, A., Katz, M., Cohen-Dvashi, H. et al. J Mol Biol (2019) 431:2095-2111. DOI 10.1016/j.jmb.2019.04.012 · PubMed

Other PDB entries of the same protein (UniProt P08669 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MJ1 1.9 Å, Native tagless Lassa virus spike complex bound at pH 8.0
9MHE 2.01 Å, Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0
9MIV 2.02 Å, Native tagless Lassa virus spike complex pH 6.0
9MJ2 2.58 Å, Flag-tag Lassa virus spike complex at pH 6.0
4ZJF 2.6 Å, Crystal structure of GP1 - the receptor binding domain of Lassa virus
7S8H 2.7 Å, Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F
9MIY 2.72 Å, Focused reconstruction of the transmembrane region of the Lassa virus spike complex
7UOV 2.75 Å, Native Lassa glycoprotein in complex with neutralizing antibodies 12.1F and 37.2D
7UOT 2.77 Å, Native Lassa glycoprotein in complex with neutralizing antibodies 8.9F and 37.2D
7TYV 2.8 Å, Structure of Lassa Virus glycoprotein (Josiah) bound to Fab 25.10C
8VCV 2.8 Å, Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody…
8VE8 2.8 Å, Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody…

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