8EJJ: Lassa virus glycoprotein complex

Lassa virus glycoprotein complex (Josiah) bound to S370.7 Fab. Determined by electron microscopy at 3.22 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 3.22 Å
Organisms: Lassa mammarenavirus, Homo sapiens
Chains: 12
Atoms: 14,862
Mol. weight: 218.05 kDa
Ligands: MAN, NAG
Released: 7 Jun 2023

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

Secondary structure: helices and β-sheets

8EJJ contains 81 α-helices and 147 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.

Chains a, b and c: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	266-268	3
β-strand	269	1	27
β-strand	271	1	28
β-strand	274	1	28
β-strand	278-280	3	27
α-helix	281	1
α-helix	282-284	3
β-strand	285	1	2
β-strand	291-293	3	27
α-helix	295-298	4
α-helix	299-302	4
α-helix	308-325	18
α-helix	327-329	3
α-helix	335-344	10
α-helix	347-358	12
β-strand	363	1	29
β-strand	368-374	7	1
β-strand	380	1	1
α-helix	381-383	3
β-strand	384-385	2	1
α-helix	386-387	2
β-strand	388-389	2	29
β-strand	392-393	2	29
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-422	23

Chains A, B and C: 7 helices, 12 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	131-142	12
α-helix	150-152	3
β-strand	153-155	3	3
β-strand	158	1	4
β-strand	161	1	4
β-strand	163-167	5	3
α-helix	184-194	11
α-helix	199-202	4
β-strand	219-226	8	3
β-strand	234-237	4	3
α-helix	239-244	6

Chains h, H and I: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	36
α-helix	17-18	2
β-strand	19-22	4	37
β-strand	37	1	38
β-strand	39-44	6	39
β-strand	51-56	6	39
β-strand	65-67	3	39
α-helix	72-75	3
β-strand	76-81	6	37
β-strand	86-91	6	37
β-strand	100-105	6	39
β-strand	109	1	38
α-helix	111B-111D	3
β-strand	118	1	39
β-strand	122-124	3	39
β-strand	125-126	2	36

Chains J, l and L: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	21
β-strand	9-12	3	22
β-strand	19-24	6	21
α-helix	38-39	2
β-strand	40-44	5	22
β-strand	51-54	4	22
β-strand	55	1	23
β-strand	66	1	23
α-helix	67-68	2
β-strand	76-80	5	21
β-strand	86-91	6	21
α-helix	96-98	3
β-strand	100-107	8	22
β-strand	116-118	3	22
β-strand	122-125	4	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein GP1	A, B, C	protein	197	Lassa mammarenavirus	P08669 (AlphaFold model)
S370.7 heavy chain Fab	H, I, h	protein	128	Homo sapiens
S370.7 light chain Fab	J, L, l	protein	107	Homo sapiens
Glycoprotein GP2	a, b, c	protein	164	Lassa mammarenavirus	P08669 (AlphaFold model)

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

>8EJJ_1 Glycoprotein GP1 (chains A, B, C)
TSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFC
NLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAAN
HCGTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSP
IGYLGLLSQRTRDIYIS

Sequence of entity 2 (H, I, h), FASTA

>8EJJ_2 S370.7 heavy chain Fab (chains H, I, h)
QVHLQQWGTGLLKPSETLSLTCAVYGGSISSYYWSWIRQPPGKGLEWIGEISHSGSTNYN
PSLKSRVTISVDTSKNQLSLKLRSVTAADTAVYYCARGRDCRSVSCYVSSPENWFDPWGQ
GTPITVSS

Sequence of entity 3 (J, L, l), FASTA

>8EJJ_3 S370.7 light chain Fab (chains J, L, l)
YELTQPPSVSVSPGQTARITCSGDALPKQYAYWYQQKPGQAPVMVIYKDSERPSGIPERF
SGSNSGTTVTLTISGVQAEDEADYYCQSADSDGTYRVFGGGTKVTVL

Sequence of entity 4 (a, b, c), FASTA

>8EJJ_4 Glycoprotein GP2 (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAPAQMSIQLINKAVNALINDQLIMKNHLRDIMCIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQ

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies. Perrett, H.R., Brouwer, P.J.M., Hurtado, J. et al. Cell Rep (2023) 42:112524-112524. DOI 10.1016/j.celrep.2023.112524 · 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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