7S8H: Lassa virus glycoprotein

Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 Jun 2022.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Lassa virus, Homo sapiens
Chains: 6
Atoms: 9,824
Mol. weight: 143.63 kDa
Ligands: NAG
Released: 1 Jun 2022

Explore 7S8H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S8H contains 54 α-helices and 113 β-strands across 6 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	27
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	28
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	28
β-strand	392-393	2	28
α-helix	394-395	2
α-helix	396-399	4
α-helix	400-420	21

Chain A: 11 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	168-170	3
α-helix	183-194	12
α-helix	199-201	3
β-strand	219-226	8	3
β-strand	237	1	3
α-helix	239-244	6
α-helix	245-247	3
α-helix	252-254	3

Chain B: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	14
β-strand	12-13	2	15
β-strand	19-26	8	14
β-strand	33-41	9	16
β-strand	45-53	9	16
β-strand	58-60	3	16
α-helix	62-64	3
β-strand	68-71	4	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-100	9	16
β-strand	101	1	17
β-strand	109	1	17
β-strand	114-115	2	16
β-strand	119-121	3	16
β-strand	122-123	2	15
α-helix	126-128	3
β-strand	129	1	18
β-strand	132-136	5	19
β-strand	149-157	9	19
β-strand	158	1	18
β-strand	163-166	4	20
β-strand	171	1	20
β-strand	175-177	3	19
α-helix	178-180	3
β-strand	181-182	2	19
β-strand	188-195	8	19
β-strand	207-211	5	20
β-strand	212	1	21
α-helix	213-215	3
β-strand	217	1	21
β-strand	220-222	3	20

Chain C: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	22
β-strand	11-14	4	23
β-strand	20-26	7	22
α-helix	29-30	2
α-helix	31-33	3
β-strand	35-40	6	23
α-helix	45-46	2
β-strand	47-51	5	23
β-strand	55-56	2	23
β-strand	64-69	6	22
β-strand	72-77	6	22
α-helix	82-84	3
β-strand	87-92	6	23
α-helix	98-99	2
β-strand	100-101	2	23
β-strand	102	1	22
β-strand	105-109	5	23
β-strand	114	1	24
α-helix	115-116	2
β-strand	117-121	5	25
α-helix	122-124	3
α-helix	125-130	6
β-strand	132-142	11	25
β-strand	143	1	24
β-strand	148-153	6	26
β-strand	156-157	2	26
β-strand	162-166	5	25
α-helix	167-170	4
β-strand	176-185	10	25
α-helix	186-191	6
β-strand	194-200	7	26
β-strand	208-213	6	26

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	4
β-strand	11-13	3	5
β-strand	19-26	8	4
α-helix	30-32	3
β-strand	34-40	7	5
β-strand	47-52	6	5
β-strand	59-61	3	5
α-helix	63-65	3
β-strand	69-74	6	4
β-strand	79-84	6	4
α-helix	89-91	3
β-strand	93-100	8	5
β-strand	113	1	5
β-strand	114	1	4
β-strand	117-121	5	5
α-helix	124-126	3
β-strand	127	1	6
β-strand	130-134	5	7
β-strand	145-155	11	7
β-strand	156	1	6
β-strand	161-164	4	8
α-helix	165-167	3
β-strand	169	1	8
β-strand	173-175	3	7
α-helix	176-178	3
β-strand	179-180	2	7
β-strand	186-195	10	7
α-helix	198-201	4
β-strand	204-210	7	8
α-helix	211-213	3
β-strand	215-221	7	8

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-13	4	10
β-strand	19-25	7	9
α-helix	31-33	3
β-strand	34-39	6	10
β-strand	46-50	5	10
β-strand	54-55	2	10
α-helix	56	1
β-strand	63-68	6	9
β-strand	71-76	6	9
α-helix	81-83	3
β-strand	86-92	7	10
β-strand	98-100	3	10
β-strand	101	1	9
β-strand	104-108	5	10
β-strand	113	1	11
β-strand	116-120	5	12
α-helix	121-123	3
α-helix	124-129	6
β-strand	131-141	11	12
β-strand	142	1	11
β-strand	147-152	6	13
β-strand	156	1	13
β-strand	161-165	5	12
α-helix	166-169	4
β-strand	175-184	10	12
α-helix	185-190	6
β-strand	193-199	7	13
β-strand	207-212	6	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G1	A	protein	201	Lassa virus	P08669 (AlphaFold model)
18.5C Fab Heavy Chain	H	protein	228	Homo sapiens
18.5C Fab Light Chain	L	protein	217	Homo sapiens
36.1F Fab Heavy Chain	B	protein	229	Homo sapiens
36.1F Fab Light Chain	C	protein	216	Homo sapiens
Glycoprotein G2	a	protein	165	Lassa virus	P08669 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7S8H_1 Glycoprotein G1 (chains A)
TSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFC
NLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAAN
HCGTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSP
IGYLCLLSQRTRDIYISRRRR

Sequence of entity 2 (H), FASTA

>7S8H_2 18.5C Fab Heavy Chain (chains H)
DEVQLVQSGGGLVRPGGSLRLSCAAAGFTFKSYSMNWVRQAPGRGLEWVSSITSGGSKTY
YADVVKGRFTVSRDNAKQSLYLQMNSLRAEDTAIYFCARSLHSTSQPSYMDVWGRKITVI
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 3 (L), FASTA

>7S8H_3 18.5C Fab Light Chain (chains L)
DDIVLTQSPGTLSLSPGERATLSCRASQSVISYYVAWYQHKGGQAPRLLIYGASSRATGV
PDRFSGSGSGTDFTLTISSLEPEDFALYYCQYYGSSPLWAFGQGTKVEIKRTVAAPSVFI
FPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSS
TLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (B), FASTA

>7S8H_4 36.1F Fab Heavy Chain (chains B)
QVQLQESGAGLVKPSETLSLSCAVSGGPFSGAYWTWIRQTPGKGLEWIGEAGRSGTTNYN
PSLKSRVTISLDTSKSQFSLKLTSVTAADTAVYFCGRRQIMSLSNLYKRPVDSWGRGTPV
IVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 5 (C), FASTA

>7S8H_5 36.1F Fab Light Chain (chains C)
EIVLTQSPGTLSLSPGERATLSCRASQSVTKNYLAWYQQKPGQAPTLVIYDASTRASGIP
DRFIGSGSGTDFTLTISRLEPEDFAVYYCHQYGSSPPYTFGRGTKLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (a), FASTA

>7S8H_6 Glycoprotein G2 (chains a)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAPAQTSIQLINKAVNALINDQLCMKNHLRDIMGIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Delineating the mechanism of anti-Lassa virus GPC-A neutralizing antibodies. Enriquez, A.S., Buck, T.K., Li, H. et al. Cell Rep (2022) 39:110841-110841. DOI 10.1016/j.celrep.2022.110841 · 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
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…
8VE8 2.8 Å, Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody…

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