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- EMDB-28182: Lassa virus glycoprotein complex (Josiah) bound to 12.1F Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-28182
TitleLassa virus glycoprotein complex (Josiah) bound to 12.1F Fab
Map data
Sample
  • Complex: Lassa mammarenavirus GPC
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: 12.1F Fab heavy chain
    • Protein or peptide: 12.1F Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
Keywordsglycoprotein complex / Lassa mammarenavirus / LASV / GPC / immune system / viral fusion protein / Lassa virus / lineage IV / Josiah / 12.1F / VIRAL PROTEIN
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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsPerrett HR / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Cell Rep / Year: 2023
Title: Structural conservation of Lassa virus glycoproteins and recognition by neutralizing antibodies.
Authors: Hailee R Perrett / Philip J M Brouwer / Jonathan Hurtado / Maddy L Newby / Lin Liu / Helena Müller-Kräuter / Sarah Müller Aguirre / Judith A Burger / Joey H Bouhuijs / Grace Gibson / ...Authors: Hailee R Perrett / Philip J M Brouwer / Jonathan Hurtado / Maddy L Newby / Lin Liu / Helena Müller-Kräuter / Sarah Müller Aguirre / Judith A Burger / Joey H Bouhuijs / Grace Gibson / Terrence Messmer / John S Schieffelin / Aleksandar Antanasijevic / Geert-Jan Boons / Thomas Strecker / Max Crispin / Rogier W Sanders / Bryan Briney / Andrew B Ward /
Abstract: Lassa fever is an acute hemorrhagic fever caused by the zoonotic Lassa virus (LASV). The LASV glycoprotein complex (GPC) mediates viral entry and is the sole target for neutralizing antibodies. ...Lassa fever is an acute hemorrhagic fever caused by the zoonotic Lassa virus (LASV). The LASV glycoprotein complex (GPC) mediates viral entry and is the sole target for neutralizing antibodies. Immunogen design is complicated by the metastable nature of recombinant GPCs and the antigenic differences among phylogenetically distinct LASV lineages. Despite the sequence diversity of the GPC, structures of most lineages are lacking. We present the development and characterization of prefusion-stabilized, trimeric GPCs of LASV lineages II, V, and VII, revealing structural conservation despite sequence diversity. High-resolution structures and biophysical characterization of the GPC in complex with GP1-A-specific antibodies suggest their neutralization mechanisms. Finally, we present the isolation and characterization of a trimer-preferring neutralizing antibody belonging to the GPC-B competition group with an epitope that spans adjacent protomers and includes the fusion peptide. Our work provides molecular detail information on LASV antigenic diversity and will guide efforts to design pan-LASV vaccines.
History
DepositionSep 16, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28182.png

Downloads & links

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Map

FileDownload / File: emd_28182.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å		1.15 Å/pix.
x 300 pix.
= 345. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.88586485 - 1.3646272
Average (Standard dev.)0.0008204746 (±0.032599583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 345.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28182_msk_1.map
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Additional map: #1

Fileemd_28182_additional_1.map
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Half map: #2

Fileemd_28182_half_map_1.map
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Half map: #1

Fileemd_28182_half_map_2.map
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Sample components

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Entire : Lassa mammarenavirus GPC

EntireName: Lassa mammarenavirus GPC
Components
  • Complex: Lassa mammarenavirus GPC
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: 12.1F Fab heavy chain
    • Protein or peptide: 12.1F Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Lassa mammarenavirus GPC

SupramoleculeName: Lassa mammarenavirus GPC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: GPC protein codon-optimized and expressed in HEK 293F cells using covalently-linked I53-50A trimerization scaffold bound to 12.1F Fab
Source (natural)Organism: Lassa mammarenavirus / Strain: Josiah
Molecular weightTheoretical: 425 KDa

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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 mammarenavirus / Strain: Mouse/Sierra Leone/Josiah/1976
Molecular weightTheoretical: 29.09843 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 RR

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 mammarenavirus / Strain: Mouse/Sierra Leone/Josiah/1976
Molecular weightTheoretical: 44.765047 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 LEWS HPQFE K

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #3: 12.1F Fab heavy chain

MacromoleculeName: 12.1F Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.650168 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGAG LLKPSETLSL SCTVDGESFN GFFWTWIRQP PGKGLEWIGE INHLASTGYN PSLKSRVTIS VDTSKNQFSL KLTSVTAAD TAVYYCARGY SYGFAWPNYH YLDVWGKGTT VTVSS

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Macromolecule #4: 12.1F Fab light chain

MacromoleculeName: 12.1F Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.851164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ETTLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQHKP GQAPRLLIYG ASKRATGIPS RFSGSGSGTD FSLTISSLEP EDFAVYYCQ HRSDWRTTFG QGTRLEIKK

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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

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Macromolecule #10: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 10 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration3.0 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time 10 s; blotting time varied between 3-7 s; blotting force of 0.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.33 e/Å2
Electron beamAcceleration voltage: 200 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
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7sgd

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 62262
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7sgd


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8ejh:
Lassa virus glycoprotein complex (Josiah) bound to 12.1F Fab

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