9R8U: Pre-glycoprotein polyprotein GP complex

Flag-tag LASV spike acidified to pH 5.0 and re-equilibrated to pH 8.0. Determined by electron microscopy at 3.3 Å resolution. Released 17 Sept 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Lassa virus Josiah
Chains: 6
Atoms: 9,380
Mol. weight: 185.03 kDa
Ligands: NAG
Released: 17 Sept 2025

Explore 9R8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9R8U contains 54 α-helices and 55 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	264-269	6
β-strand	278-280	3	4
α-helix	282-284	3
β-strand	285	1	2
β-strand	291-293	3	4
α-helix	295-300	6
α-helix	308-325	18
α-helix	334-344	11
α-helix	347-358	12
β-strand	363	1	5
β-strand	368-374	7	1
β-strand	380	1	1
α-helix	381-383	3
β-strand	384-385	2	1
β-strand	388-389	2	5
β-strand	392-393	2	5
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-424	25

Chains A and B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	1
β-strand	66-72	7	1
β-strand	73	1	2
α-helix	75-78	4
β-strand	84-87	4	3
β-strand	92-97	6	3
β-strand	101-108	8	3
α-helix	120-126	7
α-helix	131-143	13
α-helix	150-152	3
β-strand	153-156	4	3
α-helix	158-160	3
β-strand	163-167	5	3
α-helix	183-195	13
β-strand	219-226	8	3
β-strand	237	1	3
α-helix	239-245	7
α-helix	252-254	3

Chain b: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	264-269	6
β-strand	278-280	3	6
α-helix	282-284	3
β-strand	285	1	7
β-strand	291-293	3	6
α-helix	295-300	6
α-helix	308-325	18
α-helix	334-344	11
α-helix	347-358	12
β-strand	363	1	8
β-strand	368-374	7	9
β-strand	380	1	9
α-helix	381-383	3
β-strand	384-385	2	9
β-strand	388-389	2	8
β-strand	392-393	2	8
α-helix	394-395	2
α-helix	396-399	4
α-helix	400-424	25

Chain c: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	264-269	6
β-strand	278-280	3	10
α-helix	282-284	3
β-strand	285	1	11
β-strand	291-293	3	10
α-helix	295-300	6
α-helix	308-325	18
α-helix	334-344	11
α-helix	347-358	12
β-strand	363-374	12	12
β-strand	380	1	12
α-helix	381-383	3
β-strand	384-389	6	12
β-strand	392-393	2	12
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-424	25

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	12
β-strand	66-72	7	12
β-strand	73	1	11
α-helix	75-78	4
β-strand	84-87	4	14
β-strand	92-97	6	14
β-strand	101-108	8	14
α-helix	120-126	7
α-helix	131-143	13
α-helix	150-152	3
β-strand	153-156	4	14
α-helix	158-160	3
β-strand	163-167	5	14
α-helix	183-195	13
β-strand	219-225	7	14
β-strand	237	1	14
α-helix	239-245	7
α-helix	252-254	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pre-glycoprotein polyprotein GP complex	A, B, C	protein	259	Lassa virus Josiah	P08669 (AlphaFold model)
Glycoprotein G2	a, b, c	protein	244	Lassa virus Josiah	P08669 (AlphaFold model)

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

>9R8U_1 Pre-glycoprotein polyprotein GP complex (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRLL

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

>9R8U_2 Glycoprotein G2 (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAEAQMSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGKTPLGLVDLFVFSTS
FYLISIFLHLVKIPTHRHIVGKSCPKPHRLNHMGICSCGLYKQPGVPVKWKRGGGSDYKD
DDDK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

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

Primary citation

pH-induced conformational changes and inhibition of the Lassa virus spike complex. Katz, M., Cohen-Dvashi, H., Borni, S. et al. Cell Host Microbe (2025) 33:1577. DOI 10.1016/j.chom.2025.07.020 · 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
5OMI 2.56 Å, Crystal structure of GP2 from Lassa virus in a post fusion conformation
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…

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