8VCV: Lineage IV Lassa virus glycoprotein

Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (GPC-C epitope). Determined by electron microscopy at 2.8 Å resolution. Released 25 Sept 2024.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Lassa virus Josiah, Oryctolagus cuniculus
Chains: 8
Atoms: 10,466
Mol. weight: 256.54 kDa
Ligands: NAG
Released: 25 Sept 2024

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

Secondary structure: helices and β-sheets

8VCV contains 69 α-helices and 79 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	264-266	3
β-strand	278-280	3	15
α-helix	282-284	3
β-strand	285	1	2
β-strand	291-293	3	15
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	16
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	16
β-strand	392-393	2	16
α-helix	394-395	2
α-helix	396-399	4
α-helix	400-412	13

Chain A: 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	163-166	4	3
α-helix	183-194	12
α-helix	200-202	3
β-strand	219-226	8	3
β-strand	237	1	3
α-helix	239-244	6
α-helix	252-254	3

Chain b: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	278-280	3	17
β-strand	285	1	5
β-strand	291-293	3	17
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	18
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	18
β-strand	392-393	2	18
α-helix	394-395	2
α-helix	396-399	4
α-helix	400-412	13

Chain B: 8 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	76-80	5
β-strand	84-87	4	6
β-strand	92-96	5	6
β-strand	101-108	8	6
α-helix	120-126	7
α-helix	131-142	12
α-helix	150-152	3
β-strand	153-155	3	6
α-helix	158-160	3
β-strand	163-167	5	6
α-helix	183-194	12
α-helix	199-202	4
β-strand	219-226	8	6
β-strand	237	1	6
α-helix	239-245	7

Chain c: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	264-266	3
β-strand	278-280	3	19
α-helix	282-284	3
β-strand	285	1	8
β-strand	291-293	3	19
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	20
β-strand	368-374	7	7
β-strand	380	1	7
α-helix	381-383	3
β-strand	384-385	2	7
β-strand	388-389	2	20
β-strand	392-393	2	20
α-helix	394-395	2
α-helix	396-399	4
α-helix	400-412	13

Chain C: 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	75-78	4
β-strand	83-89	7	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	153-155	3	9
α-helix	158-160	3
β-strand	163-167	5	9
α-helix	183-194	12
β-strand	219-225	7	9
β-strand	237	1	9
α-helix	239-244	6
α-helix	245-247	3
α-helix	252-254	3

Chain H: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	10
α-helix	12-13	2
β-strand	18-23	6	10
β-strand	34-39	6	11
β-strand	46-51	6	11
β-strand	57-59	3	11
β-strand	67-73	7	10
β-strand	76-81	6	10
α-helix	82	1
β-strand	88-98	11	11
α-helix	99-100	2
α-helix	100F	1
β-strand	100J-101	7	11
α-helix	103-104	2
β-strand	105	1	10
α-helix	106	1
β-strand	107-109	3	11

Chain L: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	12
β-strand	12	1	13
β-strand	20-24	5	12
β-strand	33-39	7	14
β-strand	42-49	8	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-64	3	12
β-strand	71-75	5	12
β-strand	85-92	8	14
β-strand	95E-103	9	14
β-strand	105	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G1	A, B, C	protein	259	Lassa virus Josiah	P08669 (AlphaFold model)
Rabbit polyclonal Fv heavy chain	H	protein	125	Oryctolagus cuniculus
Rabbit polyclonal Fv light chain	L	protein	110	Oryctolagus cuniculus
Glycoprotein G2	a, b, c	protein	406	Lassa virus Josiah	P08669 (AlphaFold model)

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

>8VCV_1 Glycoprotein G1 (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRLL

Sequence of entity 2 (H), FASTA

>8VCV_2 Rabbit polyclonal Fv heavy chain (chains H)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXX

Sequence of entity 3 (L), FASTA

>8VCV_3 Rabbit polyclonal Fv light chain (chains L)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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

>8VCV_4 Glycoprotein G2 (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAPAQMSIQLINKAVNALINDQLIMKNHLRDIMCIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGGSGGSGGSGGSGGSE
KAAKAEEAARKMEELFKKHKIVAVLRANSVEEAIEKAVAVFAGGVHLIEITFTVPDADTV
IKALSVLKEKGAIIGAGTVTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGV
MTPTELVKAMKLGHDILKLFPGEVVGPEFVKAMKGPFPNVKFVPTGGVDLDNVCEWFDAG
VLAVGVGDALVEGDPDEVREKAKEFVEKIRGCTEGSLEWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

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
8VE8 2.8 Å, Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody…

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