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- PDB-9mt6: Structure of the Junin virus glycoprotein complex -

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Basic information

Entry
Database: PDB / ID: 9mt6
TitleStructure of the Junin virus glycoprotein complex
Components
  • JUNV GP1
  • JUNV GP2
  • Pre-glycoprotein polyprotein GP complex
KeywordsVIRAL PROTEIN / fusogen / glycoprotein / membrane / complex
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsMann, C.J. / Abraham, J.
Funding support United States, 4items
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: 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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: JUNV GP1
D: Pre-glycoprotein polyprotein GP complex
G: Pre-glycoprotein polyprotein GP complex
I: JUNV GP2
E: JUNV GP1
H: JUNV GP1
C: JUNV GP2
F: JUNV GP2
A: Pre-glycoprotein polyprotein GP complex
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,72031
Polymers166,9609
Non-polymers5,76122
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 9 molecules BEHDGAICF

#1: Protein JUNV GP1 / Pre-GP-C


Mass: 22311.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Gene: GPC, GP-C / Production host: Homo sapiens (human) / References: UniProt: P26313
#2: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 6315.510 Da / Num. of mol.: 3 / Mutation: K33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Strain: MC2 / Gene: GPC, GP-C / Production host: Homo sapiens (human) / References: UniProt: P26313
#3: Protein JUNV GP2 / Pre-GP-C


Mass: 27026.191 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus juninense / Strain: MC2 / Gene: GPC, GP-C / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P26313

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Sugars , 2 types, 16 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 6 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Glycoprotein complex from Junin virus / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mammarenavirus juninense / Strain: MC2
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50.03 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83055 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311970
ELECTRON MICROSCOPYf_angle_d0.59616218
ELECTRON MICROSCOPYf_dihedral_angle_d8.0212226
ELECTRON MICROSCOPYf_chiral_restr0.0431875
ELECTRON MICROSCOPYf_plane_restr0.0041998

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