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- EMDB-48781: JUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudo... -

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Basic information

Entry
Database: EMDB / ID: EMD-48781
TitleJUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudotyped virus membrane
Map data
Sample
  • Complex: JUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudotyped virus membrane
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: neutralizing antibody light chain
    • Protein or peptide: neutralizing antibody heavy chain
  • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Ligand: MYRISTIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsViral protein / Glycoprotein / GPC / JUNV / Junin mammarenavirus / GP1 / GP2 / signal peptide / virus membrane / antibody
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 / metal ion binding / membrane
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 speciesMammarenavirus juninense / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTaylor LJ / Sawaya MR / Castells-Graells R / Rodriguez JA
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM145388 United States
National Science Foundation (NSF, United States)DMR-1548924 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128867 United States
Howard Hughes Medical Institute (HHMI)HHMI EPI United States
Department of Defense (DOD, United States)FA9550-23-1-0281 United States
CitationJournal: Cell Rep / Year: 2025
Title: In situ insights into antibody-mediated neutralization of a pre-fusion Junin virus glycoprotein complex.
Authors: Lily J Taylor / Michael R Sawaya / Jonna B Westover / Chenyi Wang / Frederick Jimenez / Aldo J Muñoz / Julian Whitelegge / Brian B Gowen / Gustavo F Helguera / Roger Castells-Graells / Jose A Rodriguez /
Abstract: A transmembrane glycoprotein complex (GPC) decorates the Junin mammarenavirus (JUNV) that causes New World hemorrhagic fevers. We leveraged single-particle cryoelectron microscopy (cryo-EM) to image ...A transmembrane glycoprotein complex (GPC) decorates the Junin mammarenavirus (JUNV) that causes New World hemorrhagic fevers. We leveraged single-particle cryoelectron microscopy (cryo-EM) to image the full-length JUNV GPC directly on pseudotyped virus (PV) membranes and bound by two JUNV-neutralizing antibodies: Candid#1 vaccine-elicited CR1-28 and J199, a potent therapeutic against Argentine hemorrhagic fever (AHF). The 3.8 Å resolution in situ structures of the antibody-neutralized, 3-fold symmetric JUNV GPC reveal its ectodomain architecture, signal peptide-bound transmembrane region, zinc-binding luminal domain, and post-translational modifications. JUNV-GPC sequence variants highlight the functional importance of the signal peptide transmembrane helix register for virus infection and attenuating Candid#1-associated variants. Overlapping CR1-28 and J199 epitopes suggest a common receptor-blocking mechanism for JUNV neutralization, while a J199-induced, symmetric GPC reorientation may further drive its potent inhibition of JUNV lethality in mice, compared to receptor blockade alone. This underscores the utility of in situ insights into GPC function and neutralization.
History
DepositionJan 24, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48781.png

Downloads & links

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Map

FileDownload / File: emd_48781.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.58
Minimum - Maximum-3.917715 - 4.7219844
Average (Standard dev.)-0.006491213 (±0.10551148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48781_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48781_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : JUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudo...

EntireName: JUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudotyped virus membrane
Components
  • Complex: JUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudotyped virus membrane
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: neutralizing antibody light chain
    • Protein or peptide: neutralizing antibody heavy chain
  • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Ligand: MYRISTIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: JUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudo...

SupramoleculeName: JUNV GP1, GP2, SSP complex with neutralizing antibody in a pseudotyped virus membrane
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #4-#5
Source (natural)Organism: Mammarenavirus juninense

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Macromolecule #1: Pre-glycoprotein polyprotein GP complex

MacromoleculeName: Pre-glycoprotein polyprotein GP complex / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense
Molecular weightTheoretical: 6.242416 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GQFISFMQEI PTFLQEALNI ALVAVSLIAI IKGVVNLYKS GLFQFFVFLA LAGRSCT

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #2: Pre-glycoprotein polyprotein GP complex

MacromoleculeName: Pre-glycoprotein polyprotein GP complex / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense
Molecular weightTheoretical: 21.566742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AFKIGLHTEF QTVSFSMVGL FSNNPHDLPL LCTLNKSHLY IKGGNASFKI SFDDIAVLLP EYDVIIQHPA DMSWCSKSDD QIWLSQWFM NAVGHDWYLD PPFLCRNRTK TEGFIFQVNT SKTGINENYA KKFKTGMHHL YREYPDSCLD GKLCLMKAQP T SWPLQCPL DHVNTLHFLT RGKNIQLPR

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #3: Pre-glycoprotein polyprotein GP complex

MacromoleculeName: Pre-glycoprotein polyprotein GP complex / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense
Molecular weightTheoretical: 27.026191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AFFSWSLTDS SGKDTPGGYC LEEWMLVAAK MKCFGNTAVA KCNLNHDSEF CDMLRLFDYN KNAIKTLNDE TKKQVNLMGQ TINALISDN LLMKNKIREL MSVPYCNYTK FWYVNHTLSG QHSLPRCWLI KNNSYLNISD FRNDWILESD FLISEMLSKE Y SDRQGKTP ...String:
AFFSWSLTDS SGKDTPGGYC LEEWMLVAAK MKCFGNTAVA KCNLNHDSEF CDMLRLFDYN KNAIKTLNDE TKKQVNLMGQ TINALISDN LLMKNKIREL MSVPYCNYTK FWYVNHTLSG QHSLPRCWLI KNNSYLNISD FRNDWILESD FLISEMLSKE Y SDRQGKTP LTLVDICFWS TVFFTASLFL HLVGIPTHRH IRGEACPLPH RLNSLGGCRC GKYPNLKKPT VWRRGH

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #4: neutralizing antibody light chain

MacromoleculeName: neutralizing antibody light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.35974 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
QIVLTQSPAI MSASPGEKVT ITCSASSIVS YMHWFQQKPG TSPKLWIYGT SNLASGVPAR FSGSGSGTSY SLTISRMEAE DAATYYCQQ RNSYPPTFGG GTKLEIK

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Macromolecule #5: neutralizing antibody heavy chain

MacromoleculeName: neutralizing antibody heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.082606 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
VALVESGGGL VQPGGSLKLS CASGASFSNA GMSWVRQTPD RRLELVAAIN RDGDITYHPD SVKGRFTISR DNAKNTLYLQ MSSLKSEDT AMYYCAREDY YGLYFYVMDY WGQGTSVTVA

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Macromolecule #7: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 7 / Number of copies: 3 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 15 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 0.6 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279624
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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