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- EMDB-25109: Lassa virus glycoprotein construct (Josiah GPC-I53-50A) in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-25109
TitleLassa virus glycoprotein construct (Josiah GPC-I53-50A) in complex with LAVA01 antibody
Map dataGPC-I53-50A in complex with LAVA01 antibody - Main map
Sample
  • Complex: Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex with LAVA01 antibody (as Fab fragment)
    • Protein or peptide: GPC-I53-50A
    • Protein or peptide: LAVA01 mAb - Heavy Chain
    • Protein or peptide: LAVA01 mAb - Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesLassa mammarenavirus / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.41 Å
AuthorsAntanasijevic A / Brouwer PJM / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Cell Host Microbe / Year: 2022
Title: Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection.
Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Adam J Ronk / Helena Müller-Kräuter / Yasunori Watanabe / Mathieu Claireaux / Hailee R Perrett / Tom P L Bijl / Marloes Grobben / Jeffrey C ...Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Adam J Ronk / Helena Müller-Kräuter / Yasunori Watanabe / Mathieu Claireaux / Hailee R Perrett / Tom P L Bijl / Marloes Grobben / Jeffrey C Umotoy / Angela I Schriek / Judith A Burger / Khadija Tejjani / Nicole M Lloyd / Thijs H Steijaert / Marlies M van Haaren / Kwinten Sliepen / Steven W de Taeye / Marit J van Gils / Max Crispin / Thomas Strecker / Alexander Bukreyev / Andrew B Ward / Rogier W Sanders /
Abstract: The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of ...The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here, we use two-component protein nanoparticles consisting of trimeric and pentameric subunits to stabilize GPC in a trimeric conformation. These GPC nanoparticles present twenty prefusion GPC trimers on the surface of an icosahedral particle. Cryo-EM studies of GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against the lethal Lassa virus challenge in guinea pigs. Additionally, we isolated a neutralizing antibody that mapped to the putative receptor-binding site, revealing a previously undefined site of vulnerability. Collectively, these findings offer potential approaches to vaccine and therapeutic design for the Lassa virus.
History
DepositionOct 5, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25109.png

Downloads & links

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Map

FileDownload / File: emd_25109.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGPC-I53-50A in complex with LAVA01 antibody - Main map
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.009107032 - 0.01920835
Average (Standard dev.)3.956624e-05 (±0.0007075216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 370.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25109_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GPC-I53-50A in complex with LAVA01 antibody - Half Map 1

Fileemd_25109_half_map_1.map
AnnotationGPC-I53-50A in complex with LAVA01 antibody - Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GPC-I53-50A in complex with LAVA01 antibody - Half Map 2

Fileemd_25109_half_map_2.map
AnnotationGPC-I53-50A in complex with LAVA01 antibody - Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex...

EntireName: Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex with LAVA01 antibody (as Fab fragment)
Components
  • Complex: Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex with LAVA01 antibody (as Fab fragment)
    • Protein or peptide: GPC-I53-50A
    • Protein or peptide: LAVA01 mAb - Heavy Chain
    • Protein or peptide: LAVA01 mAb - Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex...

SupramoleculeName: Lassa virus glycoprotein construct(Josiah GPC-I53-50A) in complex with LAVA01 antibody (as Fab fragment)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Complex was assembled by combining GPC-I53-50A and LAVA01 Fabs
Source (natural)Organism: Lassa mammarenavirus

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Macromolecule #1: GPC-I53-50A

MacromoleculeName: GPC-I53-50A / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Lassa mammarenavirus
Molecular weightTheoretical: 73.84557 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL ...String:
MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL SHSYAGDAAN HCGTVANGVL QTFMRMAWGG SYIALDSGCG NWDCIMTSYQ YLIIQNTTWE DHCQFSRPSP IG YLGLLSQ RTRDIYISRR RRGTFTWTLS DSEGKDTPGG YCLTRWMLIE AELKCFGNTA VAKCNEKHDE EFCDMLRLFD FNK QAIQRL KAPAQMSIQL INKAVNALIN DQLIMKNHLR DIMCIPYCNY SKYWYLNHTT TGRTSLPKCW LVSNGSYLNE THFS DDIEQ QADNMITEML QKEYMERQGG SGGSGGSGGS GGSEKAAKAE EAARKMEELF KKHKIVAVLR ANSVEEAIEK AVAVF AGGV HLIEITFTVP DADTVIKALS VLKEKGAIIG AGTVTSVEQC RKAVESGAEF IVSPHLDEEI SQFCKEKGVF YMPGVM TPT ELVKAMKLGH DILKLFPGEV VGPEFVKAMK GPFPNVKFVP TGGVDLDNVC EWFDAGVLAV GVGDALVEGD PDEVREK AK EFVEKIRGCT EGSLEWSHPQ FEK

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Macromolecule #2: LAVA01 mAb - Heavy Chain

MacromoleculeName: LAVA01 mAb - Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 15.459241 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QLLSCIALSL ALVTNSQLEE SGGGLVQTEG SLTLTCTASG FSFSNNDYIC WVRQAPGKGL EWIGCIYSDY GFSFFATWAK DRFSGSKTS STTVTLQGTG LTAADTATYF CVKTYVSRFG YYIRWDYFDL WGPGTLVIVS SGQ

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Macromolecule #3: LAVA01 mAb - Light Chain

MacromoleculeName: LAVA01 mAb - Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 12.490637 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NSDQVMTQTP SPVSAAVGGT VSISCQSSKS VHNENFLSWY QQKPGQRPKL LIYRASTLAS GVPSRFKGSG SGTQFTLTIS DVQCDDAAT YYCAGGDIQS SDDVFGGGTE VVVQGDPVAP S

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
10.0 mMTris-HClTrisTris
150.0 mMNaClSodium chlorideSodium chloride

Details: TBS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 5s, Wait time 10s, Blot force 0.
DetailsThe complex was assembled by combining chemically cross-linked GPC-I53-50A with 6-fold molar excess of LAVA01 antibody (as Fab fragment).

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3098 / Average exposure time: 9.5 sec. / Average electron dose: 50.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 416326 / Details: template picker
Startup modelType of model: OTHER / Details: Map reconstructed from negative stain EM
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: Regularized likelihood
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: Regularized likelihood
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: C3 symmetry was used for refinement. Solvent mask around the complex was used for refinement.
Number images used: 8480
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5vk2

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7sgf:
Lassa virus glycoprotein construct (Josiah GPC-I53-50A) in complex with LAVA01 antibody

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