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- EMDB-48601: Structure of the Junin virus glycoprotein complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48601
TitleStructure of the Junin virus glycoprotein complex
Map data
Sample
  • Complex: Glycoprotein complex from Junin virus
    • Protein or peptide: JUNV GP1
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: JUNV GP2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
Keywordsfusogen / glycoprotein / membrane / complex / 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 juninense
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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)NIH grant 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 Junin 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_48601.png

Downloads & links

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Map

FileDownload / File: emd_48601.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.)
0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 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: 0.02
Minimum - Maximum-0.001710142 - 1.860544
Average (Standard dev.)0.00033752568 (±0.013332623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48601_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48601_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 from Junin virus

EntireName: Glycoprotein complex from Junin virus
Components
  • Complex: Glycoprotein complex from Junin virus
    • Protein or peptide: JUNV GP1
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: JUNV GP2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

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Supramolecule #1: Glycoprotein complex from Junin virus

SupramoleculeName: Glycoprotein complex from Junin virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mammarenavirus juninense / Strain: MC2

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Macromolecule #1: JUNV GP1

MacromoleculeName: JUNV GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense
Molecular weightTheoretical: 22.311578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEAFKIGLHT EFQTVSFSMV GLFSNNPHDL PLLCTLNKSH LYIKGGNASF KISFDDIAVL LPEYDVIIQH PADMSWCSKS DDQIWLSQW FMNAVGHDWY LDPPFLCRNR TKTEGFIFQV NTSKTGINEN YAKKFKTGMH HLYREYPDSC LDGKLCLMKA Q PTSWPLQC ...String:
EEAFKIGLHT EFQTVSFSMV GLFSNNPHDL PLLCTLNKSH LYIKGGNASF KISFDDIAVL LPEYDVIIQH PADMSWCSKS DDQIWLSQW FMNAVGHDWY LDPPFLCRNR TKTEGFIFQV NTSKTGINEN YAKKFKTGMH HLYREYPDSC LDGKLCLMKA Q PTSWPLQC PLDHVNTLHF LTRGKNIQLP RRSLK

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 / Strain: MC2
Molecular weightTheoretical: 6.31551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGQFISFMQE IPTFLQEALN IALVAVSLIA IIAGVVNLYK SGLFQFFVFL ALAGRSCT

UniProtKB: Pre-glycoprotein polyprotein GP complex

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Macromolecule #3: JUNV GP2

MacromoleculeName: JUNV GP2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense / Strain: MC2
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 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / 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: 50.03 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83055
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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