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- PDB-9mha: CryoEM Structure of Zaire Ebola Virus Envelope Glycoprotein GP -

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Basic information

Entry
Database: PDB / ID: 9mha
TitleCryoEM Structure of Zaire Ebola Virus Envelope Glycoprotein GP
Components
  • Envelope glycoprotein,GP1
  • GP2
KeywordsVIRAL PROTEIN / EBOV / Ebola / GP / Zaire / Mayinga / MDT-000759 / VIRUS
Function / homology
Function and homology information


symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga
Zaire (virus)
1976
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWeidle, C. / Borst, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-18-1-0001 United States
CitationJournal: To Be Published
Title: Towards a Pan-Ebola Virus Disease Nanoparticle Vaccine
Authors: Brunette, N. / Weidle, C. / Wrenn, S.P. / Fiala, B. / Ravichandran, R. / Carr, K.D. / Zak, S.E. / Zumbrun, E.E. / Murphy, M. / Chan, S. / Skotheim, R. / Borst, A.J. / Lauren, C. / Correnti, ...Authors: Brunette, N. / Weidle, C. / Wrenn, S.P. / Fiala, B. / Ravichandran, R. / Carr, K.D. / Zak, S.E. / Zumbrun, E.E. / Murphy, M. / Chan, S. / Skotheim, R. / Borst, A.J. / Lauren, C. / Correnti, C.E. / Dye, J.M. / Baker, D. / King, N.P. / Stewart, L.J.
History
DepositionDec 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: GP2
E: GP2
F: GP2
A: Envelope glycoprotein,GP1
B: Envelope glycoprotein,GP1
D: Envelope glycoprotein,GP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9489
Polymers163,1886
Non-polymers1,7603
Water00
1


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

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Components

#1: Protein GP2


Mass: 18989.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Production host: Homo sapiens (human) / Strain (production host): ExpiHEK293F / References: UniProt: Q05320
#2: Protein Envelope glycoprotein,GP1 / GP1 / 2 / GP


Mass: 35406.648 Da / Num. of mol.: 3 / Mutation: residues 313-463 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Production host: Homo sapiens (human) / Strain (production host): ExpiHEK293F / References: UniProt: Q05320
#3: 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.: 3
Source method: isolated from a genetically manipulated source
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
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: Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 foldon attached to stabilize soluble trimer
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.162507 MDa / Experimental value: NO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Source (recombinant)Organism: Homo sapiens (human) / Strain: ExpiHEK293F
Buffer solutionpH: 7.5 / Details: 20mM Tris pH 7.5 300mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtris(hydroxymethyl)aminomethane1
2300 mMSodium ChlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20mM Tris pH 7.5, 300mM NaCl
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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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: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 56.69 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3128

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Leginonimage acquisition
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.21.1_5286model refinement
14Cootmodel refinement
15UCSF ChimeraXmodel refinement
16ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 540665
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189700 / Algorithm: FOURIER SPACE / Details: Non Uniform Refinement / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: Crystal Structure 5JQ3 was used as a starting model and fit with Chimera. Structure was further refined in Coot, Phenix, ChimeraX, Isolde
Atomic model buildingPDB-ID: 5JQ3

5jq3


Accession code: 5JQ3 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.05 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046341
ELECTRON MICROSCOPYf_angle_d0.5898644
ELECTRON MICROSCOPYf_dihedral_angle_d13.5952340
ELECTRON MICROSCOPYf_chiral_restr0.045997
ELECTRON MICROSCOPYf_plane_restr0.0041114

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