8P4T: The spike complex of the Lujo Virus

The spike complex of the Lujo Virus. Determined by electron microscopy at 2.96 Å resolution. Released 12 Jun 2024.

Method: Electron microscopy
Resolution: 2.96 Å
Organism: Mammarenavirus lujoense
Chains: 9
Atoms: 9,976
Mol. weight: 173.69 kDa
Ligands: NAG
Released: 12 Jun 2024

Explore 8P4T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P4T contains 60 α-helices and 48 β-strands across 9 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, b and c: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	246-248	3	3
α-helix	257-261	5
α-helix	270-287	18
α-helix	292-297	6
α-helix	303-306	4
α-helix	309-321	13
β-strand	325	1	4
β-strand	330-336	7	3
β-strand	342	1	3
α-helix	343-345	3
β-strand	346-347	2	3
β-strand	350-351	2	4
β-strand	354-355	2	4
α-helix	356-357	2
α-helix	358-360	3
α-helix	362-387	26
α-helix	390-408	19

Chains A, B and C: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	61-64	4
β-strand	65-72	8	1
α-helix	74-76	3
β-strand	82-84	3	2
β-strand	89-92	4	2
β-strand	95-102	8	2
β-strand	110	1	2
α-helix	113-119	7
α-helix	121-134	14
β-strand	143-145	3	2
β-strand	153-158	6	2
α-helix	163-173	11
β-strand	183-190	8	2
β-strand	199	1	2
α-helix	201-212	12
α-helix	215-217	3

Chains SA, SB and SC: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-7	5
α-helix	8-11	4
α-helix	15-34	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein	A, B, C	protein	163	Mammarenavirus lujoense	C5ILC1 (AlphaFold model)
Glycoprotein	a, b, c	protein	247	Mammarenavirus lujoense	C5ILC1 (AlphaFold model)
Glycoprotein	SA, SB, SC	protein	58	Mammarenavirus lujoense	C5ILC1 (AlphaFold model)

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

>8P4T_1 Glycoprotein (chains A, B, C)
SSLLSGFNLETVHFNMSLLSSIPMVSEQQHCIQHNHSSITFSLLTNKSDLEKCNFTRLQA
VDRVIFDLFREFHHRVGDFPVTSDLKCSHNTSYRVIEYEVTKESLPRLQEAVSTLFPDLH
LSEDRFLQIQAHDDKNCTGLHPLNYLRLLKENSETHYKVRKLM

Sequence of entity 2 (a, b, c), FASTA

>8P4T_2 Glycoprotein (chains a, b, c)
KLFQWSLSDETGSPLPGGHCLERWLIFASDIKCFDNAAIAKCNKEHDEEFCDMLRLFDYN
KASIAKLRGEASSSINLLSGRINAIISDTLLMRSSLKRLMGIPYCNYTKFWYLNHTKLGI
HSLPRCWLVSNGSYLNETKFTHDMEDEADKLLTEMLKKEYVRRQEKTPITLMDILMFSVS
FYMFSVTLCICNIPTHRHITGLPCPKPHRLRKNGTCACGFFKSINRSTGWAKHGGDYKDD
DDKGSGT

Sequence of entity 3 (SA, SB, SC), FASTA

>8P4T_3 Glycoprotein (chains SA, SB, SC)
MGQIVAVFQAIPEILNEAINIVIIVIIMFTLIKGVFNLYKSGLFQLVIFLLLCGKRCD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	21

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

Primary citation

The structure of the Lujo virus spike complex. Eilon-Ashkenazy, M., Cohen-Dvashi, H., Borni, S. et al. Nat Commun (2024) 15:7175-7175. DOI 10.1038/s41467-024-51606-0 · PubMed

Other PDB entries of the same protein (UniProt C5ILC1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GH8 2.44 Å, Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of…

Browse structure collections

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