8TYE: Lassa GPC

Lassa GPC (strain Josiah) bound to rabbit polyclonal fusion-peptide-targeting antibody FP-1. Determined by electron microscopy at 3.8 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Oryctolagus cuniculus, Lassa virus (strain Mouse/Sierra Leone/Josiah/1976), Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
Chains: 8
Atoms: 9,921
Mol. weight: 252.45 kDa
Ligands: NAG
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8TYE contains 51 α-helices and 66 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	280	1	18
β-strand	285	1	9
β-strand	291	1	18
α-helix	295-301	7
α-helix	309-325	17
α-helix	327-329	3
α-helix	335-338	4
α-helix	347-358	12
β-strand	363-374	12	8
α-helix	382-383	2
β-strand	384-389	6	8
β-strand	392-393	2	8
α-helix	394-395	2
α-helix	400-412	13

Chain A: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	61	1	8
β-strand	66-72	7	8
β-strand	73	1	9
α-helix	75-79	5
β-strand	84-86	3	10
β-strand	93-96	4	10
β-strand	97	1	11
β-strand	101	1	11
β-strand	102-108	7	10
α-helix	120-126	7
α-helix	131-142	12
β-strand	153-156	4	10
α-helix	158-160	3
β-strand	163-167	5	10
α-helix	183-194	12
β-strand	219-225	7	10
α-helix	239-244	6
α-helix	246-248	3

Chain b: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	278-280	3	19
β-strand	285	1	13
β-strand	291-293	3	19
α-helix	295-303	9
α-helix	308-325	18
α-helix	327-329	3
α-helix	335-339	5
α-helix	347-358	12
β-strand	363	1	20
β-strand	368-374	7	12
β-strand	380	1	12
α-helix	381-383	3
β-strand	384-385	2	12
β-strand	388-389	2	20
β-strand	392-393	2	20
α-helix	394-395	2
α-helix	397-399	3
α-helix	400-413	14

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	12
β-strand	66-72	7	12
β-strand	73	1	13
α-helix	75-80	6
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	131-142	12
β-strand	153-156	4	14
α-helix	158-160	3
β-strand	163-167	5	14
α-helix	183-194	12
β-strand	219-225	7	14
β-strand	237	1	14
α-helix	239-245	7

Chain c: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	264-266	3
β-strand	275	1	15
β-strand	277	1	15
β-strand	278-280	3	16
β-strand	291-293	3	16
α-helix	295-300	6
α-helix	308-324	17
α-helix	327-329	3
α-helix	335-344	10
α-helix	347-358	12
β-strand	363	1	17
β-strand	368-374	7	5
β-strand	380	1	5
α-helix	381-383	3
β-strand	384-385	2	5
β-strand	388-389	2	17
β-strand	392-393	2	17
α-helix	394-395	2
α-helix	400-413	14

Chain C: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	5
β-strand	66-72	7	5
α-helix	76-79	4
β-strand	84-85	2	6
β-strand	87	1	7
β-strand	95-96	2	6
β-strand	102-108	7	6
α-helix	120-126	7
α-helix	131-142	12
β-strand	153-156	4	6
α-helix	158-160	3
β-strand	163-167	5	6
α-helix	183-194	12
β-strand	219-225	7	6
β-strand	234	1	7
α-helix	239-246	8
α-helix	252-254	3

Chain H: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	35A-38	4	1
β-strand	65-68	4	2
α-helix	70-72	3
β-strand	76-79	4	2
α-helix	88	1
β-strand	89-92	4	1

Chain L: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
α-helix	5-6	2
β-strand	25	1	3
β-strand	35-37	3	4
β-strand	48-49	2	4
α-helix	50-52	3
β-strand	53-54	2	4
α-helix	55	1
β-strand	86-88	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polyclonal Fv heavy chain	H	protein	116	Oryctolagus cuniculus
Polyclonal Fv light chain	L	protein	102	Oryctolagus cuniculus
Glycoprotein GP1	A, B, C	protein	259	Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)	P08669 (AlphaFold model)
Glycoprotein GP2	a, b, c	protein	406	Lassa virus (strain Mouse/Sierra Leone/Josiah/1976), Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)	P08669 (AlphaFold model), Q9WXS1 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8TYE_1 Polyclonal Fv heavy chain (chains H)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 2 (L), FASTA

>8TYE_2 Polyclonal Fv light chain (chains L)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (A, B, C), FASTA

>8TYE_3 Glycoprotein GP1 (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRLL

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

>8TYE_4 Glycoprotein GP2 (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	14

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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