9MHE: Native tagless Lassa virus spike complex

Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0. Determined by electron microscopy at 2.01 Å resolution. Released 27 Aug 2025.

Method: Electron microscopy
Resolution: 2.01 Å
Organisms: Lassa virus Josiah, Homo sapiens
Chains: 12
Atoms: 17,624
Mol. weight: 337.81 kDa
Ligands: A1BK9, NAG
Released: 27 Aug 2025

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

Secondary structure: helices and β-sheets

9MHE contains 78 α-helices and 129 β-strands across 12 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	264-268	5
β-strand	278-280	3	1
α-helix	282-284	3
β-strand	285	1	2
β-strand	291-293	3	1
α-helix	295-303	9
α-helix	308-325	18
α-helix	334-344	11
α-helix	347-358	12
β-strand	363	1	3
β-strand	368-374	7	4
β-strand	380	1	4
α-helix	381-383	3
β-strand	384-385	2	4
β-strand	388-389	2	3
β-strand	392-393	2	3
α-helix	394-395	2
α-helix	396-425	30
α-helix	428-446	19

Chain A: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-13	3
α-helix	18-36	19
β-strand	61-62	2	4
β-strand	66-72	7	4
β-strand	73	1	2
α-helix	75-78	4
β-strand	84-87	4	5
β-strand	92-97	6	5
β-strand	101-108	8	5
α-helix	120-126	7
α-helix	131-143	13
α-helix	150-152	3
β-strand	153-156	4	5
α-helix	158-160	3
β-strand	163-167	5	5
α-helix	183-194	12
α-helix	199-202	4
β-strand	219-226	8	5
β-strand	237	1	5
α-helix	239-245	7
α-helix	252-254	3

Chain b: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	264-268	5
β-strand	278-280	3	12
β-strand	285	1	7
β-strand	291-293	3	12
α-helix	295-301	7
α-helix	308-325	18
α-helix	334-344	11
α-helix	347-358	12
β-strand	363	1	13
β-strand	368-374	7	6
β-strand	380	1	6
α-helix	381-383	3
β-strand	384-385	2	6
β-strand	388-389	2	13
β-strand	392-393	2	13
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-423	24
α-helix	428-448	21

Chain B: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-15	5
α-helix	18-36	19
β-strand	61-62	2	6
β-strand	66-72	7	6
β-strand	73	1	7
α-helix	75-80	6
β-strand	84-87	4	8
β-strand	92-97	6	8
β-strand	101-108	8	8
α-helix	120-126	7
α-helix	131-143	13
α-helix	150-152	3
β-strand	153-156	4	8
α-helix	158-160	3
β-strand	163-167	5	8
α-helix	183-194	12
α-helix	199-202	4
β-strand	219-226	8	8
β-strand	237	1	8
α-helix	239-245	7
α-helix	252-254	3

Chain c: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	264-268	5
β-strand	278-280	3	14
β-strand	285	1	10
β-strand	291-293	3	14
α-helix	295-301	7
α-helix	308-325	18
α-helix	334-344	11
α-helix	347-358	12
β-strand	363	1	15
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	15
β-strand	392-393	2	15
α-helix	394-395	2
α-helix	396-425	30
α-helix	428-448	21

Chain C: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-15	5
α-helix	18-36	19
β-strand	61-62	2	9
β-strand	66-72	7	9
β-strand	73	1	10
α-helix	75-80	6
β-strand	84-87	4	11
β-strand	92-97	6	11
β-strand	101-108	8	11
α-helix	120-126	7
α-helix	131-143	13
α-helix	150-152	3
β-strand	153-156	4	11
α-helix	158-160	3
β-strand	163-167	5	11
α-helix	179-181	3
α-helix	183-194	12
α-helix	200-202	3
β-strand	219-226	8	11
β-strand	237	1	11
α-helix	239-245	7
α-helix	252-254	3

Chain D: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	27
β-strand	11-12	2	28
β-strand	18-25	8	27
β-strand	33-39	7	23
β-strand	46-51	6	23
β-strand	57-59	3	23
β-strand	67-72	6	27
β-strand	77-82	6	27
α-helix	87-89	3
β-strand	91-101	11	23
α-helix	107	1
β-strand	108-114	7	23
β-strand	118-120	3	23
β-strand	121-122	2	28

Chains E and G: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-12	3	22
β-strand	19-25	7	21
β-strand	32	1	23
β-strand	34-38	5	22
β-strand	45-49	5	22
β-strand	53-54	2	22
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-92	8	22
β-strand	95-98	4	22
β-strand	102-105	4	22

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G2	a, b, c	protein	232	Lassa virus Josiah	P08669 (AlphaFold model)
Glycoprotein G1	A, B, C	protein	259	Lassa virus Josiah	P08669 (AlphaFold model)
12.1F Heavy chain	D, F, H	protein	249	Homo sapiens
12.1F Light chain	E, G, L	protein	214	Homo sapiens

Sequence of entity 1 (a, b, c), FASTA

>9MHE_1 Glycoprotein G2 (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAEAQMSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGKTPLGLVDLFVFSTS
FYLISIFLHLVKIPTHRHIVGKSCPKPHRLNHMGICSCGLYKQPGVPVKWKR

Sequence of entity 2 (A, B, C), FASTA

>9MHE_2 Glycoprotein G1 (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRLL

Sequence of entity 3 (D, F, H), FASTA

>9MHE_3 12.1F Heavy chain (chains D, F, H)
QVQLQESGAGLLKPSETLSLSCTVDGESFNGFFWTWIRQPPGKGLEWIGEINHLASTGYN
PSLKSRVTISVDTSKNQFSLKLTSVTAADTAVYYCARGYSYGFAWPNYHYLDVWGKGTTV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHGGDYKDDDD
KGTENLYFQ

Sequence of entity 4 (E, G, L), FASTA

>9MHE_4 12.1F Light chain (chains E, G, L)
EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQHKPGQAPRLLIYGASKRATGIPS
RFSGSGSGTDFSLTISSLEPEDFAVYYCQHRSDWRTTFGQGTRLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
A1BK9	(4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2…	C27 H30 N2 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

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) 33:1577-1588.e7. 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
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…
8VE8 2.8 Å, Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody…

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