7s8h

Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F

Method: X-RAY DIFFRACTION D_max: 153.7 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein G1

Lassa virus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 18 其他Polymer 27 PDB declaration: octadecameric（18） Consistent with protein copy count	Chain A； UniProt 59–259 Chain a； UniProt 260–424	Mutation：G243C, Residues 256-259 mutated from RRLL to RRRR Mutation：E329P, M332T, I350C	18.5C Fab Heavy Chain × 3 18.5C Fab Light Chain × 3 36.1F Fab Heavy Chain × 3 36.1F Fab Light Chain × 3 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；293.15 K；0.1 M Tris, pH 8.0, 1.25 M LiCl and 15% PEG 8k	Resolution 2.70 Å R-free 0.251

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7S8H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FT2 Sub-tomogram averaging of Lassa virus glycoprotein spike from virus- like particles at pH 5 Deposited 2016-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 75–237（163 aa） Fragment：RECEPTOR BINDING DOMAIN, UNP RESIDUES 75-237	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer 50 MM BUFFER OF SUCCINIC ACID, DIHYDROGEN PHOSPHATE AND GLYCINE (SPG)；pH 5.2；50 MM BUFFER OF SUCCINIC ACID, DIHYDROGEN PHOSPHATE AND GLYCINE (SPG) cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；VITRIFICATION 1 -- CRYOGEN- ETHANE-PROPANE MIXTURE, HUMIDITY- 80, TEMPERATURE- 120, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING.,	Resolution 16.40 Å
5VK2 Structural basis for antibody-mediated neutralization of Lassa virus Deposited 2017-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–259（259 aa） Fragment：UNP residues 1-259 Chain B 1–259（259 aa） Fragment：UNP residues 1-259 Chain C 1–259（259 aa） Fragment：UNP residues 1-259 Chain a 260–423（164 aa） Fragment：UNP residues 260-423 Chain b 260–423（164 aa） Fragment：UNP residues 260-423 Chain c 260–423（164 aa） Fragment：UNP residues 260-423	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；296 K；0.1M Tris pH 8, 15-18% PEG 3350 and 0.1M-0.3M magnesium acetate	Resolution 3.20 Å R-free 0.231
6P95 Structure of Lassa virus glycoprotein in complex with Fab 25.6A Deposited 2019-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–433（174 aa） Chain b 260–433（174 aa） Chain c 260–433（174 aa）	Mutation：R207C, L258R, L259RG Mutation：R207C, L258R, L259RG Mutation：R207C, L258R, L259RG Mutation：G360P, M332T, E329C Mutation：G360P, M332T, E329C Mutation：G360P, M332T, E329C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；0.1 M Tris pH 8, 15-18% PEG 3350 and 0.1 M-0.3 M magnesium acetate	Resolution 3.50 Å R-free 0.247
7PUY Structure of the membrane soluble spike complex from the Lassa virus in a C3-symmetric map Deposited 2021-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7PVD Structure of the membrane soluble spike complex from the Lassa virus in a C1-symmetric map focused on the ectodomain Deposited 2021-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7TYV Structure of Lassa Virus glycoprotein (Josiah) bound to Fab 25.10C Deposited 2022-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–423（164 aa） Chain b 260–423（164 aa） Chain c 260–423（164 aa）	Mutation：R207C, Residues 256-259 mutated from RRLL to RRRR Mutation：R207C, Residues 256-259 mutated from RRLL to RRRR Mutation：R207C, Residues 256-259 mutated from RRLL to RRRR Mutation：E329P, M332T, G360C Mutation：E329P, M332T, G360C Mutation：E329P, M332T, G360C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7UOT Native Lassa glycoprotein in complex with neutralizing antibodies 8.9F and 37.2D Deposited 2022-04-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
7UOV Native Lassa glycoprotein in complex with neutralizing antibodies 12.1F and 37.2D Deposited 2022-04-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.75 Å
8EJD Structure of lineage IV Lassa virus glycoprotein complex (strain Josiah) Deposited 2022-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Mutation：R207C, L258R, L259R Mutation：R207C, L258R, L259R Mutation：R207C, L258R, L259R Mutation：E329P, G360C Mutation：E329P, G360C Mutation：E329P, G360C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s; blotting time varied between 3-7 s; blotting force of 0	Resolution 3.80 Å
8EJH Lassa virus glycoprotein complex (Josiah) bound to 12.1F Fab Deposited 2022-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Mutation：R207C, L258R, L259R Mutation：R207C, L258R, L259R Mutation：R207C, L258R, L259R Mutation：E329P, G360C Mutation：E329P, G360C Mutation：E329P, G360C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MAN alpha-D-mannopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s; blotting time varied between 3-7 s; blotting force of 0	Resolution 3.71 Å
8EJI Lassa virus glycoprotein complex (Josiah) bound to 19.7E Fab Deposited 2022-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Mutation：R207C, L258R, L259R Mutation：R207C, L258R, L259R Mutation：R207C, L258R, L259R Mutation：E328P, G359C Mutation：E328P, G359C Mutation：E328P, G359C	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS cryo-EM vitrification conditions Cryogen ETHANE；Wait time 10 s; blotting time varied between 3-7 s; blotting force of 0	Resolution 3.81 Å
8T5C Lassa GPC Trimer in complex with Fab 8.11G and nanobody D5 Deposited 2023-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 59–257（199 aa） Chain B 59–257（199 aa） Chain C 59–257（199 aa） Chain a 260–418（159 aa） Chain b 260–418（159 aa） Chain c 260–418（159 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
8TYC Lassa GPC (strain Josiah) bound to rabbit polyclonal base-targeting antibody Base-1 Deposited 2023-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–423（164 aa） Chain b 260–423（164 aa） Chain c 260–423（164 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8TYE Lassa GPC (strain Josiah) bound to rabbit polyclonal fusion-peptide-targeting antibody FP-1 Deposited 2023-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8VCV Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (GPC-C epitope) Deposited 2023-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8VE8 Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (GP1-A epitope) Deposited 2023-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9CJ7 Lineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F Deposited 2024-07-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9CJ8 Lineage IV Lassa virus glycoprotein (Josiah) in complex with rabbit polyclonal antibody (LAVA01-like epitope) Deposited 2024-07-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
9CK7 Lineage IV Lassa virus glycoprotein (Josiah) in complex with polyclonal antibody (GPC-A epitope) from rabbit 187 Deposited 2024-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9CK8 Lineage IV Lassa virus glycoprotein (Josiah) in complex with polyclonal antibody (GPC-A epitope) from rabbit 189 Deposited 2024-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–424（165 aa） Chain b 260–424（165 aa） Chain c 260–424（165 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.04 Å
9MHE Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 Deposited 2024-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 UNX UNKNOWN LIGAND × 2 A1BK9 (4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.01 Å
9MIV Native tagless Lassa virus spike complex pH 6.0 Deposited 2024-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 UNX UNKNOWN LIGAND × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.02 Å
9MIY Focused reconstruction of the transmembrane region of the Lassa virus spike complex Deposited 2024-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–58（58 aa） Chain B 1–58（58 aa） Chain C 1–58（58 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.72 Å
9MJ1 Native tagless Lassa virus spike complex bound at pH 8.0 Deposited 2024-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 UNX UNKNOWN LIGAND × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.90 Å
9MJ2 Flag-tag Lassa virus spike complex at pH 6.0 Deposited 2024-12-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 59–259（201 aa） Chain B 59–259（201 aa） Chain C 59–259（201 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 UNX UNKNOWN LIGAND × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å
9R8U Flag-tag LASV spike acidified to pH 5.0 and re-equilibrated to pH 8.0 Deposited 2025-05-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–259（259 aa） Chain B 1–259（259 aa） Chain C 1–259（259 aa） Chain a 260–491（232 aa） Chain b 260–491（232 aa） Chain c 260–491（232 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 UNX UNKNOWN LIGAND × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLYC_LASSJ
Isoform	—
PDB entities	1, 6
Chains and sequence ranges	Author chain A； PDBConstruct 1–201； UniProt 59–259 Author chain a； PDBConstruct 1–165； UniProt 260–424

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7s8h
Deposition date deposition_date	2021-09-17
Structure title title	Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F
Keywords keywords	;Lassa virus, pre-fusion glycoprotein, Fab fragment, antibody-mediated neutralization, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex ;; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	44.83 Å
Radius of gyration Rg (electron density) rg_electron	45.20 Å
Forward intensity I(0) i0	295133000.00
Molecular weight molecular_weight	138980.0 kDa
Excluded volume excluded_volume	173130 Å³
Envelope volume envelope_volume	253130 Å³
Hydration-shell volume shell_volume	48430 Å³
Envelope diameter envelope_diameter	162.3 Å
Shell Rg shell_rg	47.27 Å
Envelope Rg envelope_rg	44.93 Å
Shape Rg shape_rg	45.20 Å
Total Rg total_rg	45.31 Å
Total atoms total_atoms	9760
Residues n_residues	1215
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	153.7 Å
Rg (real space) rg_real	45.17 Å
Rg uncertainty (real space) rg_real_error	1.82 Å
I(0) (real space) i0_real	2.9510e+08
I(0) uncertainty (real space) i0_real_error	5.5360e+06
Rg (reciprocal space) rg_reciprocal	44.84 Å
I(0) (reciprocal space) i0_reciprocal	295000000.0000
Solution quality estimate total_estimate	0.8217
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.5 Å
Skewness Skewness skewness	0.422
Kurtosis Kurtosis kurtosis	-0.522
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20070000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.714; Smooth: 0.630

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Description description	Glycoprotein G1
Molecular weight formula_weight	22928.0 kDa
Mutation mutation	G243C, Residues 256-259 mutated from RRLL to RRRR
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9824

TSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGRGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLCLLSQRTRDIYISRRRR

来源 Source

来源生物 organism	Lassa virus
NCBI Class编号 ncbi_taxonomy_id	11622
宿主生物 host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	18.5C Fab Heavy Chain
Molecular weight formula_weight	24309.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DEVQLVQSGGGLVRPGGSLRLSCAAAGFTFKSYSMNWVRQAPGRGLEWVSSITSGGSKTYYADVVKGRFTVSRDNAKQSLYLQMNSLRAEDTAIYFCARSLHSTSQPSYMDVWGRKITVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	18.5C Fab Light Chain
Molecular weight formula_weight	23654.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DDIVLTQSPGTLSLSPGERATLSCRASQSVISYYVAWYQHKGGQAPRLLIYGASSRATGVPDRFSGSGSGTDFTLTISSLEPEDFALYYCQYYGSSPLWAFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	36.1F Fab Heavy Chain
Molecular weight formula_weight	24174.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLQESGAGLVKPSETLSLSCAVSGGPFSGAYWTWIRQTPGKGLEWIGEAGRSGTTNYNPSLKSRVTISLDTSKSQFSLKLTSVTAADTAVYFCGRRQIMSLSNLYKRPVDSWGRGTPVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 5 Entity 5 polymer

Description description	36.1F Fab Light Chain
Molecular weight formula_weight	23671.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

EIVLTQSPGTLSLSPGERATLSCRASQSVTKNYLAWYQQKPGQAPTLVIYDASTRASGIPDRFIGSGSGTDFTLTISRLEPEDFAVYYCHQYGSSPPYTFGRGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 6 Entity 6 polymer

Description description	Glycoprotein G2
Molecular weight formula_weight	19117.7 kDa
Mutation mutation	E329P, M332T, I350C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a

GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIQRLKAPAQTSIQLINKAVNALINDQLCMKNHLRDIMGIPYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQG

来源 Source

来源生物 organism	Lassa virus
NCBI Class编号 ncbi_taxonomy_id	11622
宿主生物 host_organism	Drosophila melanogaster

Entity 7 Entity 7 branched

Description description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	5

Entity 9 Entity 9 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 10 Entity 10 branched

Description description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1057.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 11 Entity 11 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

▼

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	7s8hB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s8hB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s8hC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s8hC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s8hH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s8hH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s8hL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s8hL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	163.058 Å
Unit-cell length b length_b	163.058 Å
Unit-cell length c length_c	173.548 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	trigonal

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	47.180 Å
R factor r_factor	—
R_work r_work	0.2175
R_free r_free	0.2508

fit	/app/data/saxs_computation/s8/7s8h/7s8h.fit
pddf	/app/data/pr_computation/s8/7s8h/7s8h.pr.out
profile	/app/data/saxs_computation/s8/7s8h/7s8h.dat

Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F

1. Protein Identity and Related Structures Protein Identity & Related Structures

Glycoprotein G1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (12)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

来源 Source

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 branched

Entity 10 Entity 10 branched

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)