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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: To Be Published
Title: Structure of the Machupo virus glycoprotein complex
Authors: Mann CJ / Abraham J
History
DepositionJan 10, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing 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
Brightness
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48598_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48598_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 : 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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