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- EMDB-48598: Structure of the Machupo virus glycoprotein complex -

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Basic information

Entry
Database: EMDB / ID: EMD-48598
TitleStructure of the Machupo virus glycoprotein complex
Map data
Sample
  • Complex: Glycoprotein complex of Machupo virus
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
KeywordsFusogen / glycoprotein / Complex / membrane / 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 / 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 machupoense
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMann CJ / Abraham J
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP5OD023084 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI700245 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32GM144273 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Microbiol / Year: 2025
Title: Molecular organization of the New World arenavirus spike glycoprotein complex.
Authors: Colin J Mann / Pan Yang / Daniel Olal / Xiaoyi Fan / Katherine Nabel Smith / Lars E Clark / Florian Krammer / Yuemin Bian / Jonathan Abraham /
Abstract: Of the multiple arenaviruses that cause haemorrhagic fevers in the Americas, all lack reliable therapeutic options, and only one has a vaccine. The arenavirus glycoprotein complex (GPC) binds ...Of the multiple arenaviruses that cause haemorrhagic fevers in the Americas, all lack reliable therapeutic options, and only one has a vaccine. The arenavirus glycoprotein complex (GPC) binds cellular receptors and mediates pH-dependent fusion of viral and host cell membranes during entry. GPC comprises GP1, GP2 and stable signal peptide (SSP) subunits. SSP remains associated with the mature glycoprotein complex and regulates pH-dependent membrane fusion through an unclear mechanism. We report cryo-EM structures of Junin virus and Machupo virus GPC stabilized in the prefusion conformation using an amino acid substitution in the transmembrane region of SSP at 3.0 Å and 2.9 Å resolution, respectively. Mutational analyses, cell-cell fusion assays and molecular dynamics simulations reveal how contacts in the membrane-proximal and transmembrane regions of GPC regulate pH-dependent membrane fusion. The structures may aid in the design of therapeutic antibody cocktails, small-molecule inhibitors and vaccines against arenaviruses.
History
DepositionJan 10, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48598.png

Downloads & links

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Map

FileDownload / File: emd_48598.map.gz / Format: CCP4 / Size: 421.9 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.)
0.73 Å/pix.
x 480 pix.
= 350.4 Å		0.73 Å/pix.
x 480 pix.
= 350.4 Å		0.73 Å/pix.
x 480 pix.
= 350.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0017358533 - 1.8973867
Average (Standard dev.)0.00045564503 (±0.0150683485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 350.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_48598_additional_1.map
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Half map: #1

Fileemd_48598_half_map_1.map
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Half map: #2

Fileemd_48598_half_map_2.map
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Sample components

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Entire : Glycoprotein complex of Machupo virus

EntireName: Glycoprotein complex of Machupo virus
Components
  • Complex: Glycoprotein complex of Machupo virus
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Protein or peptide: Pre-glycoprotein polyprotein GP complex
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: Glycoprotein complex of Machupo virus

SupramoleculeName: Glycoprotein complex of Machupo virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3
Source (natural)Organism: Mammarenavirus machupoense / Strain: Carvallo

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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 machupoense / Strain: Carvallo
Molecular weightTheoretical: 6.351606 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGQLISFFQE IPVFLQEALN IALVAVSLIA VIAGIINLYK SGLFQFIFFL LLAGRSCS

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 machupoense
Molecular weightTheoretical: 23.528803 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DGTFKIGLHT EFQSVTLTMQ RLLANHSNEL PSLCMLNNSF YYMRGGVNTF LIRVSDISVL MKEYDVSIYE PEDLGNCLNK SDSSWAIHW FSNALGHDWL MDPPMLCRNK TKKEGSNIQF NISKADDARV YGKKIRNGMR HLFRGFHDPC EEGKVCYLTI N QCGDPSSF ...String:
DGTFKIGLHT EFQSVTLTMQ RLLANHSNEL PSLCMLNNSF YYMRGGVNTF LIRVSDISVL MKEYDVSIYE PEDLGNCLNK SDSSWAIHW FSNALGHDWL MDPPMLCRNK TKKEGSNIQF NISKADDARV YGKKIRNGMR HLFRGFHDPC EEGKVCYLTI N QCGDPSSF DYCGVNHLSK CQFDHVNTLH FLVRSKTHLN FERSLK

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 machupoense
Molecular weightTheoretical: 27.117402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AFFSWSLTDS SGKDMPGGYC LEEWMLIAAK MKCFGNTAVA KCNQNHDSEF CDMLRLFDYN KNAIKTLNDE AKKEINLLSQ AVNALISDN LLMKNKIKEL MSIPYCNYTK FWYVNHTLTG QHTLPRCWLI RNGSYLNTSE FRNDWILESD HLISEMLSKE Y AERQGKTP ...String:
AFFSWSLTDS SGKDMPGGYC LEEWMLIAAK MKCFGNTAVA KCNQNHDSEF CDMLRLFDYN KNAIKTLNDE AKKEINLLSQ AVNALISDN LLMKNKIKEL MSIPYCNYTK FWYVNHTLTG QHTLPRCWLI RNGSYLNTSE FRNDWILESD HLISEMLSKE Y AERQGKTP ITLVDICFWS TIFFTASLFL HLVGIPTHRH LKGEACPLPH KLDSFGGCRC GKYPRLKKPT IWHKRH

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 53.43 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31197
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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