9CJ7: Lineage IV Lassa virus glycoprotein

Lineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F. Determined by electron microscopy at 3.0 Å resolution. Released 25 Sept 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Lassa virus Josiah, Homo sapiens
Chains: 8
Atoms: 11,501
Mol. weight: 300.38 kDa
Ligands: NAG
Released: 25 Sept 2024

Explore 9CJ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CJ7 contains 63 α-helices and 81 β-strands across 8 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: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	264-267	4
β-strand	278-280	3	12
α-helix	282-284	3
β-strand	285	1	5
β-strand	291-293	3	12
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	13
β-strand	368-374	7	4
β-strand	380	1	4
α-helix	381-383	3
β-strand	384-385	2	4
α-helix	386-387	2
β-strand	388-389	2	13
β-strand	392-393	2	13
α-helix	394-395	2
α-helix	397-399	3
α-helix	400-419	20

Chain A: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	4
β-strand	66-72	7	4
β-strand	73	1	5
α-helix	75-78	4
β-strand	84-87	4	6
β-strand	92-97	6	6
β-strand	101-108	8	6
α-helix	120-126	7
α-helix	131-142	12
α-helix	150-152	3
β-strand	153-156	4	6
α-helix	158-160	3
β-strand	163-167	5	6
α-helix	183-194	12
β-strand	219-226	8	6
β-strand	237	1	6
α-helix	239-246	8

Chain b: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	278-280	3	14
β-strand	285	1	8
β-strand	291-293	3	14
α-helix	295-298	4
α-helix	299-302	4
α-helix	308-325	18
α-helix	327-329	3
α-helix	336-344	9
α-helix	347-358	12
β-strand	363-374	12	7
β-strand	380	1	7
β-strand	384-388	5	7
β-strand	393	1	7
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-419	20

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	7
β-strand	66-72	7	7
β-strand	73	1	8
α-helix	75-80	6
β-strand	84-87	4	9
β-strand	92-97	6	9
β-strand	101-108	8	9
α-helix	120-126	7
α-helix	131-142	12
α-helix	150-152	3
β-strand	153-156	4	9
α-helix	158-160	3
β-strand	163-167	5	9
α-helix	168-170	3
α-helix	183-194	12
α-helix	200-202	3
β-strand	219-226	8	9
β-strand	237	1	9
α-helix	239-245	7

Chain c: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	278-280	3	10
α-helix	282-284	3
β-strand	285	1	2
β-strand	291-293	3	10
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	11
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	11
β-strand	392-393	2	11
α-helix	400-419	20

Chain C: 9 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	131-142	12
α-helix	150-152	3
β-strand	153-155	3	3
α-helix	158-160	3
β-strand	163-167	5	3
α-helix	183-194	12
α-helix	199-201	3
β-strand	219-226	8	3
β-strand	237	1	3
α-helix	239-246	8
α-helix	252-254	3

Chain H: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
α-helix	17	1
β-strand	18-25	8	15
β-strand	34-39	7	17
β-strand	46-51	6	17
β-strand	57-59	3	17
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-95	8	17
α-helix	100-100E	6
α-helix	100G-100J	4
β-strand	100U-103	4	17
β-strand	107-109	3	17
β-strand	110-111	2	16

Chain L: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	18
β-strand	5	1	19
β-strand	9-13	4	20
β-strand	19-24	6	19
α-helix	27-30B	6
β-strand	34-38	5	20
β-strand	45-48	4	20
β-strand	49	1	21
β-strand	53	1	21
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	85-92	8	20
β-strand	95A-98	4	20
β-strand	99	1	18
β-strand	102-106	5	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G1	A, B, C	protein	259	Lassa virus Josiah	P08669 (AlphaFold model)
Glycoprotein G2	a, b, c	protein	420	Lassa virus Josiah	P08669 (AlphaFold model)
Fv region of 8.9F heavy chain	H	protein	293	Homo sapiens
Fv region of 8.9F light chain	L	protein	237	Homo sapiens

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

>9CJ7_1 Glycoprotein G1 (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRLL

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

>9CJ7_2 Glycoprotein G2 (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAPAQMSIQLINKAVNALINDQLIMKNHLRDIMCIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGGSGGSGGSGGSGGSE
KAAKAEEAARKMEELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTV
IKALSVLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGV
MTPTELVKAMKLGHDILKLFPGEVVGPEFVKAMKGPFPNVKFVPTGGVDLDNVCEWFDAG
VLAVGVGDALVEGDPDEVREKAKEFVEKIRGCTEGSLEHHHHHHGGLNDIFEAQKIEWHE

Sequence of entity 3 (H), FASTA

>9CJ7_3 Fv region of 8.9F heavy chain (chains H)
METDTLLLWVLLLWVPGSTGDQGTLRESGPGLVRPSETLSLTCGVSGYSISSGYYWGWIR
QPPGKGLEWIGNIYRSGSTYYNPSLKSRVTVSIDTSKNQFSLKLNSVTAADTAVYYCARS
GIKVADDYYYEMDVWGQGTDDYSYAMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGG
TAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTY
ICNVNHKPSNTKVDKRVEPKSCGSGWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 4 (L), FASTA

>9CJ7_4 Fv region of 8.9F light chain (chains L)
METDTLLLWVLLLWVPGSTGDQAGLTQPASVSGSPGQSITISCTAANSDIGDFNFVSWYQ
QRPDKAPKLMVYEVSSRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCTSYTSSSTF
VFGTGTKVTVLGQPKANPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPV
KAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses. Brouwer, P.J.M., Perrett, H.R., Beaumont, T. et al. Cell Rep (2024) 43:114708-114708. DOI 10.1016/j.celrep.2024.114708 · 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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