7UOT: Native Lassa glycoprotein

Native Lassa glycoprotein in complex with neutralizing antibodies 8.9F and 37.2D. Determined by electron microscopy at 2.77 Å resolution. Released 2 Nov 2022.

Method: Electron microscopy
Resolution: 2.77 Å
Organisms: Lassa virus, Homo sapiens
Chains: 14
Atoms: 16,834
Mol. weight: 292.03 kDa
Released: 2 Nov 2022

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

Secondary structure: helices and β-sheets

7UOT contains 76 α-helices and 158 β-strands across 14 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	278-280	3	5
β-strand	285	1	2
β-strand	291-293	3	5
α-helix	295-299	5
α-helix	300-302	3
α-helix	308-325	18
α-helix	335-340	6
α-helix	341-343	3
α-helix	347-358	12
β-strand	363	1	6
β-strand	368-374	7	1
β-strand	380	1	1
β-strand	384-385	2	1
α-helix	386-387	2
β-strand	388-389	2	6
β-strand	392-393	2	6
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-415	16

Chain A: 8 helices, 12 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	120-125	6
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	207	1	4
β-strand	213	1	4
β-strand	219-226	8	3
β-strand	234-237	4	3
α-helix	239-244	6

Chain b: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	278-280	3	15
β-strand	285	1	13
β-strand	291-293	3	15
α-helix	295-299	5
α-helix	300-302	3
α-helix	308-325	18
α-helix	335-339	5
α-helix	347-359	13
β-strand	363	1	16
β-strand	368-374	7	12
β-strand	380	1	12
α-helix	381-383	3
β-strand	384-385	2	12
α-helix	386-387	2
β-strand	388-389	2	16
β-strand	392-393	2	16
α-helix	394-395	2
α-helix	396-398	3
α-helix	400-415	16

Chain B: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	60	1
β-strand	61-62	2	12
β-strand	66-72	7	12
β-strand	73	1	13
β-strand	84-87	4	14
β-strand	92-97	6	14
β-strand	101-108	8	14
α-helix	121-125	5
α-helix	131-142	12
α-helix	150-152	3
β-strand	153-156	4	14
α-helix	158-160	3
β-strand	163-167	5	14
α-helix	183-194	12
α-helix	199-203	5
β-strand	219-226	8	14
β-strand	237	1	14
α-helix	239-246	8

Chain c: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	278-280	3	25
β-strand	285	1	23
β-strand	291-293	3	25
α-helix	295-298	4
α-helix	299-302	4
α-helix	308-325	18
α-helix	335-340	6
α-helix	347-358	12
β-strand	363	1	26
β-strand	368-374	7	22
β-strand	380	1	22
α-helix	381-383	3
β-strand	384-385	2	22
α-helix	386-387	2
β-strand	388-389	2	26
β-strand	392-393	2	26
α-helix	396-398	3
α-helix	400-415	16

Chain C: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	22
β-strand	66-72	7	22
β-strand	73	1	23
α-helix	75-78	4
β-strand	83-87	5	24
β-strand	92-97	6	24
β-strand	101-108	8	24
α-helix	121-125	5
α-helix	131-142	12
α-helix	150-152	3
β-strand	153-156	4	24
α-helix	158-160	3
β-strand	163-166	4	24
α-helix	183-194	12
α-helix	200-203	4
β-strand	219-226	8	24
β-strand	237	1	24
α-helix	239-244	6

Chain H: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	33
β-strand	11	1	34
β-strand	18-25	8	33
α-helix	29-31	3
β-strand	34-40	7	35
β-strand	47-53	7	35
β-strand	58-60	3	35
α-helix	65-67	3
β-strand	68-73	6	33
β-strand	78-83	6	33
α-helix	88-90	3
β-strand	92-99	8	35
α-helix	104-109	6
β-strand	125-128	4	35
β-strand	132-134	3	35
β-strand	135	1	34

Chain L: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	36
β-strand	9-11	3	37
β-strand	17-24	8	36
α-helix	26-28	3
β-strand	36-40	5	37
β-strand	47-50	4	37
β-strand	51	1	38
β-strand	55	1	38
β-strand	64-69	6	36
β-strand	72-78	7	36
α-helix	82-84	3
β-strand	87-93	7	37
β-strand	99-101	3	37
β-strand	102	1	36
β-strand	105-108	4	37

6 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)
Glycoprotein G2	a, b, c	protein	232	Lassa virus	P08669 (AlphaFold model)
37.2D light chain (variable domain)	P, R, T	protein	105	Homo sapiens
37.2D heavy chain (variable domain)	O, Q, S	protein	126	Homo sapiens
8.9F heavy chain (variable domain)	H	protein	136	Homo sapiens
8.9F light chain (variable domain)	L	protein	109	Homo sapiens

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

>7UOT_1 Glycoprotein G1 (chains A, B, C)
MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTS
LYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNL
SDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHC
GTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIG
YLGLLSQRTRDIYISRRLL

Sequence of entity 2 (a, b, c), FASTA

>7UOT_2 Glycoprotein G2 (chains a, b, c)
GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFN
KQAIQRLKAEAQTSIQLINKAVNALINDQLIMKNHLRDIMGIPYCNYSKYWYLNHTTTGR
TSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQGKTPLGLVDLFVFSTS
FYLISIFLHLVKIPTHRHIVGKSCPKPHRLNHMGICSCGLYKQPGVPVKWKR

Sequence of entity 3 (P, R, T), FASTA

>7UOT_3 37.2D light chain (variable domain) (chains P, R, T)
ETTLTQSPATLSVSPGETATLSCRASQNVINNLAWYQQKPGQAPRLLIYGASTRATGIPA
RFSGSGSGTEFTLTISSMQSEDFAVYYCQQYNDWPRSFGQGTRLD

Sequence of entity 4 (O, Q, S), FASTA

>7UOT_4 37.2D heavy chain (variable domain) (chains O, Q, S)
EVQLVQSGAEVKKPGASVKVSCKASGYTFTKYGISWVRQAPGQGLEWMGWISAFNGYTRY
GQRFQGKVTMTTDTSTNTASLEVRTLTSNDTAVYYCARQYPDQYSSSGWPRLFAMDVWGQ
GTTVTV

Sequence of entity 5 (H), FASTA

>7UOT_5 8.9F heavy chain (variable domain) (chains H)
QGTLRESGPGLVRPSETLSLTCGVSGYSISSGYYWGWIRQPPGKGLEWIGNIYRSGSTYY
NPSLKSRVTVSIDTSKNQFSLKLNSVTAADTAVYYCARSGIKVADDYYYEMDVWGQGTDD
YSYAMDVWGQGTTVTV

Sequence of entity 6 (L), FASTA

>7UOT_6 8.9F light chain (variable domain) (chains L)
QAVLTQPASVSGSPGQSITISCTAANSDIGDFAFVSWYQQRPDKAPKLMVYEVSSRPSGV
SNRFSGSKSGNTASLTISGLQAEDEADYYCTSYTSSSTFVFGTGTKVTV

Primary citation

A cocktail of protective antibodies subverts the dense glycan shield of Lassa virus. Li, H., Buck, T., Zandonatti, M. et al. Sci Transl Med (2022) 14:eabq0991-eabq0991. DOI 10.1126/scitranslmed.abq0991 · 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
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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