7TYV: Lassa Virus glycoprotein

Structure of Lassa Virus glycoprotein (Josiah) bound to Fab 25.10C. Determined by electron microscopy at 2.8 Å resolution. Released 1 Jun 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Lassa virus, Homo sapiens
Chains: 12
Atoms: 17,306
Mol. weight: 305.33 kDa
Ligands: NAG
Released: 1 Jun 2022

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

Secondary structure: helices and β-sheets

7TYV contains 60 α-helices and 176 β-strands across 12 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: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	40
β-strand	285	1	2
β-strand	291-292	2	40
α-helix	295-299	5
α-helix	300-302	3
α-helix	308-323	16
α-helix	335-340	6
α-helix	347-358	12
β-strand	363	1	41
β-strand	368-374	7	1
β-strand	380	1	1
β-strand	384-385	2	1
β-strand	388-389	2	41
β-strand	392-393	2	41
α-helix	400-416	17

Chain A: 6 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	76-78	3
β-strand	84-89	6	3
β-strand	92-97	6	3
β-strand	101-108	8	3
α-helix	120-126	7
α-helix	131-143	13
β-strand	154-156	3	3
α-helix	158-160	3
β-strand	163-166	4	3
α-helix	184-194	11
β-strand	219-225	7	3
β-strand	237	1	3
α-helix	239-245	7

Chain b: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	42
β-strand	285	1	5
β-strand	291-292	2	42
α-helix	295-299	5
α-helix	308-324	17
α-helix	335-340	6
α-helix	347-358	12
β-strand	363	1	43
β-strand	368-374	7	4
β-strand	380	1	4
β-strand	384-385	2	4
β-strand	388	1	43
β-strand	393	1	43
α-helix	400-416	17

Chain B: 6 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	76-78	3
β-strand	84-87	4	6
β-strand	92-97	6	6
β-strand	101-108	8	6
α-helix	121-126	6
α-helix	131-143	13
β-strand	154-156	3	6
α-helix	158-160	3
β-strand	163-167	5	6
α-helix	184-194	11
β-strand	219-223	5	6
β-strand	237	1	6
α-helix	239-245	7

Chain c: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	279-280	2	44
β-strand	285	1	9
β-strand	291-292	2	44
α-helix	295-298	4
α-helix	299-302	4
α-helix	308-325	18
α-helix	335-340	6
α-helix	341-343	3
α-helix	347-358	12
β-strand	363-372	10	8
β-strand	384-389	6	8
β-strand	392-393	2	8
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-416	17

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	7
β-strand	66-67	2	7
β-strand	68-72	5	8
β-strand	73	1	9
α-helix	76-78	3
β-strand	84-89	6	10
β-strand	92-97	6	10
β-strand	101-108	8	10
α-helix	121-126	6
α-helix	131-141	11
β-strand	154-156	3	10
α-helix	158-160	3
β-strand	163-166	4	10
α-helix	184-194	11
β-strand	219-225	7	10
β-strand	237	1	10
α-helix	239-245	7

Chain D: 4 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-12	3	12
β-strand	18-24	7	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-101	10	12
β-strand	106-110	5	12
β-strand	115-119	5	12
α-helix	126-127	2
β-strand	128-131	4	13
β-strand	148-153	6	13
β-strand	159-162	4	14
β-strand	172-173	2	13
β-strand	177-178	2	13
β-strand	184-189	6	13
α-helix	195-198	4
β-strand	202-208	7	14
β-strand	213-219	7	14

Chain E: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	9-11	3	16
β-strand	18-24	7	15
β-strand	33-37	5	16
β-strand	44-48	5	16
β-strand	52-53	2	16
β-strand	61-66	6	15
β-strand	69-74	6	15
β-strand	84-89	6	16
β-strand	94-95	2	16
β-strand	99-102	4	16
β-strand	108	1	17
β-strand	111-115	5	18
α-helix	119-124	6
β-strand	126-136	11	18
β-strand	137	1	17
β-strand	141-147	7	19
β-strand	156-160	5	18
α-helix	161-164	4
β-strand	170-179	10	18
α-helix	180-183	4
β-strand	188-195	8	19
β-strand	202-207	6	19

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G1	A, B, C	protein	259	Lassa virus	P08669 (AlphaFold model)
25.10C Fab Heavy Chain	D, G, H	protein	226	Homo sapiens
25.10C Fab Light Chain	E, K, L	protein	233	Homo sapiens
Glycoprotein G2	a, b, c	protein	164	Lassa virus	P08669 (AlphaFold model)

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

>7TYV_1 Glycoprotein G1 (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRRR

Sequence of entity 2 (D, G, H), FASTA

>7TYV_2 25.10C Fab Heavy Chain (chains D, G, H)
QVQLQESGGGLVKPGGSLRLSCTASGFNFNKYNMNWVRQAPGKGLEWVSSISALSTYIYY
ADSLKGRFTVSRDNAKNSLFLQMNSLRDDDTAVYYCAREIRRASTWSADLWGRGTLVTVS
SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

Sequence of entity 3 (E, K, L), FASTA

>7TYV_3 25.10C Fab Light Chain (chains E, K, L)
METDTLLLWVLLLWVPGSTGDDIQMTQSPSSLSASVGDRVIITCRASQSISSSLNWYQQK
PGKAPKLLIYAAVNLETGVPSRFSGSGFGTDFTLAISNVQPEDFATYYCQQSDTRTFGRG
TKLDVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQE
SVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

>7TYV_4 Glycoprotein G2 (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAPAQTSIQLINKAVNALINDQLIMKNHLRDIMCIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	13

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
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
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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