SAXSdb — 5vk2

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

Pre-glycoprotein polyprotein GP complex

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 × 12 其他Polymer 20 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–259 Chain B； UniProt 1–259 Chain C； UniProt 1–259 Chain a； UniProt 260–423 Chain b； UniProt 260–423 Chain c； UniProt 260–423	Fragment：UNP residues 1-259 Fragment：UNP residues 260-423	Fab 37.7H heavy chain × 3 Fab 37.7H light chain × 3 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 × 11 ;alpha-D-mannopyranose-(1-3)-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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 3 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

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 5VK2	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
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 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 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
7S8H Structure of Lassa virus glycoprotein bound to Fab 18.5C and Fab 36.1F Deposited 2021-09-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 59–259（201 aa） Chain a 260–424（165 aa）	Mutation：G243C, Residues 256-259 mutated from RRLL to RRRR Mutation：E329P, M332T, I350C	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
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–259； UniProt 1–259 Author chain B； PDBConstruct 1–259； UniProt 1–259 Author chain C； PDBConstruct 1–259； UniProt 1–259 Author chain a； PDBConstruct 1–164； UniProt 260–423 Author chain b； PDBConstruct 1–164； UniProt 260–423 Author chain c； PDBConstruct 1–164； UniProt 260–423

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5vk2
Deposition date deposition_date	2017-04-20
Structure title title	Structural basis for antibody-mediated neutralization of Lassa virus
Keywords keywords	Lassa, glycoprotein, arenavirus, antibody, 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	48.83 Å
Radius of gyration Rg (electron density) rg_electron	49.34 Å
Forward intensity I(0) i0	1075720000.00
Molecular weight molecular_weight	266270.0 kDa
Excluded volume excluded_volume	331110 Å³
Envelope volume envelope_volume	454530 Å³
Hydration-shell volume shell_volume	80428 Å³
Envelope diameter envelope_diameter	176.5 Å
Shell Rg shell_rg	49.15 Å
Envelope Rg envelope_rg	50.41 Å
Shape Rg shape_rg	49.37 Å
Total Rg total_rg	49.23 Å
Total atoms total_atoms	18672
Residues n_residues	2313
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	167.4 Å
Rg (real space) rg_real	49.09 Å
Rg uncertainty (real space) rg_real_error	2.18 Å
I(0) (real space) i0_real	1.0760e+09
I(0) uncertainty (real space) i0_real_error	2.2440e+07
Rg (reciprocal space) rg_reciprocal	48.83 Å
I(0) (reciprocal space) i0_reciprocal	1075000000.0000
Solution quality estimate total_estimate	0.8539
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.3 Å
Skewness Skewness skewness	0.454
Kurtosis Kurtosis kurtosis	-0.333
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	121700000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.699

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Pre-glycoprotein polyprotein GP complex
Molecular weight formula_weight	29098.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	18672

MGQIVTFFQEVPHVIEEVMNIVLIALSVLAVLKGLYNFATCGLVGLVTFLLLCGRSCTTSLYKGVYELQTLELNMETLNMTMPLSCTKNNSHHYIMVGNETGLELTLTNTSIINHKFCNLSDAHKKNLYDHALMSIISTFHLSIPNFNQYEAMSCDFNGGKISVQYNLSHSYAGDAANHCGTVANGVLQTFMRMAWGGSYIALDSGCGNWDCIMTSYQYLIIQNTTWEDHCQFSRPSPIGYLGLLSQRTRDIYISRRRR

来源 Source

来源生物 organism	Lassa virus
通用名 common_name	LASV
NCBI Class编号 ncbi_taxonomy_id	11622
宿主生物 host_organism	Drosophila

Entity 2 Entity 2 polymer

Description description	Pre-glycoprotein polyprotein GP complex
Molecular weight formula_weight	19116.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b,c

GTFTWTLSDSEGKDTPGGYCLTRWMLIEAELKCFGNTAVAKCNEKHDEEFCDMLRLFDFNKQAIQRLKAPAQTSIQLINKAVNALINDQLIMKNHLRDIMCIPYCNYSKYWYLNHTTTGRTSLPKCWLVSNGSYLNETHFSDDIEQQADNMITEMLQKEYMERQ

来源 Source

来源生物 organism	Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)
通用名 common_name	LASV
NCBI Class编号 ncbi_taxonomy_id	11622
宿主生物 host_organism	Drosophila

Entity 3 Entity 3 polymer

Description description	Fab 37.7H heavy chain
Molecular weight formula_weight	24342.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,H

DEVQLVQSGGGLVKAGGSLRLSCAASGFTFSTYSMNWIRQAPGKGLEWVASISSRSGSHINYVDSVKGRFTISRDNARDLLYLQMNSLRVDDSALYYCARDRRSGTSPLPLDVWGQGTTVTVFSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

来源 Source

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

Entity 4 Entity 4 polymer

Description description	Fab 37.7H light chain
Molecular weight formula_weight	23103.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,L

DQSALTQPASVSGSPGQSITISCTGTGSDIGGYNFVSWYQQYPGKAPKLIIYEVRIRASGVSNRFSGSKSGNTASLTISGLQAEDEADYYCNSYSIHSPWVFGGGTKLTVLRQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

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

Entity 5 Entity 5 branched

Description description	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	586.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 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	syn
Copy count entity_count	11

Entity 7 Entity 7 branched

Description description	;alpha-D-mannopyranose-(1-3)-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	syn
Copy count entity_count	3

Entity 8 Entity 8 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	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	11

▼

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	5vk2D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2G02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vk2L02
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	152.697 Å
Unit-cell length b length_b	152.697 Å
Unit-cell length c length_c	456.738 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	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.201 Å
Low-resolution limit resolution_low	49.602 Å
R factor r_factor	0.1908
R_work r_work	0.1886
R_free r_free	0.2313

fit	/app/data/saxs_computation/vk/5vk2/5vk2.fit
pddf	/app/data/pr_computation/vk/5vk2/5vk2.pr.out
profile	/app/data/saxs_computation/vk/5vk2/5vk2.dat

Structural basis for antibody-mediated neutralization of Lassa virus

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

Pre-glycoprotein polyprotein GP complex

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 (9)

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 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

7. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)