8TYC: Lassa GPC

Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1. Determined by electron microscopy at 3.3 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Lassa virus, Oryctolagus cuniculus, Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)
Chains: 8
Atoms: 10,628
Mol. weight: 255.62 kDa
Ligands: NAG
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8TYC contains 63 α-helices and 75 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	16
α-helix	282-284	3
β-strand	285	1	2
β-strand	291-293	3	16
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	17
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	17
β-strand	392-393	2	17
α-helix	394-395	2
α-helix	396-399	4
α-helix	400-419	20

Chain A: 8 helices, 11 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
β-strand	118	1	3
α-helix	120-126	7
α-helix	131-142	12
α-helix	150-152	3
β-strand	153-156	4	3
α-helix	158-160	3
β-strand	163-167	5	3
α-helix	183-194	12
α-helix	199-202	4
β-strand	219-226	8	3
β-strand	237	1	3
α-helix	239-245	7

Chain b: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	264-268	5
β-strand	278-280	3	18
α-helix	282-284	3
β-strand	285	1	5
β-strand	291-293	3	18
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	348-358	11
β-strand	363-374	12	4
β-strand	380	1	4
α-helix	381-383	3
β-strand	384-388	5	4
β-strand	393	1	4
α-helix	394-395	2
α-helix	400-419	20

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	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	131-141	11
α-helix	150-152	3
β-strand	153-155	3	6
α-helix	158-160	3
β-strand	163-167	5	6
α-helix	184-194	11
α-helix	199-202	4
β-strand	219-224	6	6
β-strand	237	1	6
α-helix	239-244	6

Chain c: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
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	363-374	12	7
β-strand	380	1	7
α-helix	381-383	3
β-strand	384-389	6	7
β-strand	392-393	2	7
α-helix	394-395	2
α-helix	397-399	3
α-helix	400-419	20

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	75-80	6
β-strand	84-87	4	9
β-strand	92-97	6	9
β-strand	101-108	8	9
α-helix	123-126	4
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
α-helix	199-202	4
β-strand	219-226	8	9
β-strand	237	1	9
α-helix	239-246	8
α-helix	252-254	3

Chain H: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	10
α-helix	29-31	3
β-strand	33-40	8	11
β-strand	43-51	9	11
β-strand	58-59	2	11
β-strand	67-69	3	10
β-strand	76-82	7	10
α-helix	84-86	3
β-strand	88-93	6	11
α-helix	105	1
β-strand	106-109	4	11

Chain L: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	12
β-strand	11	1	13
β-strand	19-24	6	12
β-strand	34-39	6	14
β-strand	42-49	8	14
β-strand	52-53	2	14
β-strand	63-64	2	12
β-strand	68	1	15
β-strand	70	1	15
β-strand	71-75	5	12
β-strand	85-87	3	14
β-strand	102	1	14
β-strand	104	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G1	A, B, C	protein	259	Lassa virus	P08669 (AlphaFold model)
Polyclonal antibody Base-1 heavy chain	H	protein	108	Oryctolagus cuniculus
Polyclonal antibody Base-1 light chain	L	protein	107	Oryctolagus cuniculus
Glycoprotein G2, 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase…	a, b, c	protein	406	Lassa virus, Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)	P08669 (AlphaFold model), Q9WXS1 (AlphaFold model)

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

>8TYC_1 Glycoprotein G1 (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRLL

Sequence of entity 2 (H), FASTA

>8TYC_2 Polyclonal antibody Base-1 heavy chain (chains H)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (L), FASTA

>8TYC_3 Polyclonal antibody Base-1 light chain (chains L)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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

>8TYC_4 Glycoprotein G2, 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase fusion protein (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	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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