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- PDB-9mt2: Structure of the Machupo virus glycoprotein complex -

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Basic information

Entry
Database: PDB / ID: 9mt2
TitleStructure of the Machupo virus glycoprotein complex
Components(Pre-glycoprotein polyprotein GP ...) x 3
KeywordsVIRAL PROTEIN / Fusogen / glycoprotein / Complex / membrane
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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)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, C.J. / Abraham, J.
History
DepositionJan 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: FSC / Part number: 2 / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)178,83336
Polymers170,9939
Non-polymers7,83927
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Pre-glycoprotein polyprotein GP ... , 3 types, 9 molecules ADGBEHCFI

#1: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 6351.606 Da / Num. of mol.: 3 / Mutation: K33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus machupoense / Strain: Carvallo / Gene: GPC / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8AZ57
#2: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 23528.803 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus machupoense / Gene: GPC / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8AZ57
#3: Protein Pre-glycoprotein polyprotein GP complex / Pre-GP-C


Mass: 27117.402 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus machupoense / Gene: GPC / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8AZ57

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Sugars , 3 types, 21 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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.: 3
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
#6: 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.: 12 / 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

#7: 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 of Machupo virus / Type: COMPLEX / Entity ID: #1, #3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mammarenavirus machupoense / Strain: Carvallo
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: 53.43 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31197 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212150
ELECTRON MICROSCOPYf_angle_d0.47416416
ELECTRON MICROSCOPYf_dihedral_angle_d5.1072256
ELECTRON MICROSCOPYf_chiral_restr0.0381893
ELECTRON MICROSCOPYf_plane_restr0.0042025

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