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- EMDB-45624: Lineage IV Lassa virus glycoprotein (Josiah) in complex with mono... -

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Basic information

Entry
Database: EMDB / ID: EMD-45624
TitleLineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F
Map data
Sample
  • Complex: Lineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: Fv region of 8.9F heavy chain
    • Protein or peptide: Fv region of 8.9F light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLassa / monoclonal antibody / 8.9F / glycoprotein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 speciesOryctolagus cuniculus (rabbit) / Lassa virus Josiah / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBrouwer PJM / Perrett HR / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI171438 United States
CitationJournal: Cell Rep / Year: 2024
Title: Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses.
Authors: Philip J M Brouwer / Hailee R Perrett / Tim Beaumont / Haye Nijhuis / Sabine Kruijer / Judith A Burger / Ilja Bontjer / Wen-Hsin Lee / James A Ferguson / Martin Schauflinger / Helena Müller- ...Authors: Philip J M Brouwer / Hailee R Perrett / Tim Beaumont / Haye Nijhuis / Sabine Kruijer / Judith A Burger / Ilja Bontjer / Wen-Hsin Lee / James A Ferguson / Martin Schauflinger / Helena Müller-Kräuter / Rogier W Sanders / Thomas Strecker / Marit J van Gils / Andrew B Ward /
Abstract: Lassa fever continues to be a major public health burden in West Africa, yet effective therapies or vaccines are lacking. The isolation of protective neutralizing antibodies against the Lassa virus ...Lassa fever continues to be a major public health burden in West Africa, yet effective therapies or vaccines are lacking. The isolation of protective neutralizing antibodies against the Lassa virus glycoprotein complex (GPC) justifies the development of vaccines that can elicit strong neutralizing antibody responses. However, Lassa vaccine candidates have generally been unsuccessful at doing so, and the associated antibody responses to these vaccines remain poorly characterized. Here, we establish an electron microscopy-based epitope mapping workflow that enables high-resolution structural characterization of polyclonal antibodies to the GPC. By applying this method to rabbits vaccinated with a recombinant GPC vaccine and a GPC-derived virus-like particle, we reveal determinants of neutralization that involve epitopes of the GPC-A competition cluster. Furthermore, by identifying undescribed immunogenic off-target epitopes, we expose the challenges that recombinant GPC vaccines face. By enabling detailed polyclonal antibody characterization, our work ushers in a next generation of more rational Lassa vaccine design.
History
DepositionJul 5, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45624.png

Downloads & links

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Map

FileDownload / File: emd_45624.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 313.5 Å		1.05 Å/pix.
x 300 pix.
= 313.5 Å		1.05 Å/pix.
x 300 pix.
= 313.5 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.41926914 - 1.2097986
Average (Standard dev.)0.0006549865 (±0.030963901)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 313.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45624_msk_1.map
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Additional map: #1

Fileemd_45624_additional_1.map
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Half map: #1

Fileemd_45624_half_map_1.map
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Half map: #2

Fileemd_45624_half_map_2.map
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Sample components

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Entire : Lineage IV Lassa virus glycoprotein (Josiah) in complex with mono...

EntireName: Lineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F
Components
  • Complex: Lineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: Fv region of 8.9F heavy chain
    • Protein or peptide: Fv region of 8.9F light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Lineage IV Lassa virus glycoprotein (Josiah) in complex with mono...

SupramoleculeName: Lineage IV Lassa virus glycoprotein (Josiah) in complex with monoclonal antibody 8.9F
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Glycoprotein G1

MacromoleculeName: Glycoprotein G1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Molecular weightTheoretical: 29.010352 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 LL

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #2: Glycoprotein G2

MacromoleculeName: Glycoprotein G2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Molecular weightTheoretical: 46.421793 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAP AQMSIQLINK AVNALINDQ LIMKNHLRDI MCIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGGSG ...String:
GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAP AQMSIQLINK AVNALINDQ LIMKNHLRDI MCIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGGSG GSGGSGGSGG SEKAAKAEEA ARKMEELFKK HKIVAVLRAN SVEEAIEKAV AVFAGGVHLI EITFTVPDAD TV IKALSVL KEKGAIIGAG TVTSVEQCRK AVESGAEFIV SPHLDEEISQ FCKEKGVFYM PGVMTPTELV KAMKLGHDIL KLF PGEVVG PEFVKAMKGP FPNVKFVPTG GVDLDNVCEW FDAGVLAVGV GDALVEGDPD EVREKAKEFV EKIRGCTEGS LEHH HHHHG GLNDIFEAQK IEWHE

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #3: Fv region of 8.9F heavy chain

MacromoleculeName: Fv region of 8.9F heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.428758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DQGTLRESGP GLVRPSETLS LTCGVSGYSI SSGYYWGWIR QPPGKGLEWI GNIYRSGSTY YNPSLKSRV TVSIDTSKNQ FSLKLNSVTA ADTAVYYCAR SGIKVADD(TYS)(TYS) (TYS)EMDVWGQGT DDYSYAMDV WGQGTTVTVS ...String:
METDTLLLWV LLLWVPGSTG DQGTLRESGP GLVRPSETLS LTCGVSGYSI SSGYYWGWIR QPPGKGLEWI GNIYRSGSTY YNPSLKSRV TVSIDTSKNQ FSLKLNSVTA ADTAVYYCAR SGIKVADD(TYS)(TYS) (TYS)EMDVWGQGT DDYSYAMDV WGQGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGT QTYICNVNHK PSNTKVDKRV EPKSCGSGWS HPQFEKGGGS GGGSGGSAWS HPQFEK

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Macromolecule #4: Fv region of 8.9F light chain

MacromoleculeName: Fv region of 8.9F light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.244908 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DQAGLTQPAS VSGSPGQSIT ISCTAANSDI GDFNFVSWYQ QRPDKAPKLM VYEVSSRPSG VSNRFSGSK SGNTASLTIS GLQAEDEADY YCTSYTSSST FVFGTGTKVT VLGQPKANPT VTLFPPSSEE LQANKATLVC L ISDFYPGA ...String:
METDTLLLWV LLLWVPGSTG DQAGLTQPAS VSGSPGQSIT ISCTAANSDI GDFNFVSWYQ QRPDKAPKLM VYEVSSRPSG VSNRFSGSK SGNTASLTIS GLQAEDEADY YCTSYTSSST FVFGTGTKVT VLGQPKANPT VTLFPPSSEE LQANKATLVC L ISDFYPGA VTVAWKADSS PVKAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration4.0 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Low-pass filtered map of GPCysR4 (7SGD) with the I53-50A scaffold added (7SGE)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73222
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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