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- EMDB-48271: CryoEM Structure of Zaire Ebola Virus Envelope Glycoprotein GP -

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Basic information

Entry
Database: EMDB / ID: EMD-48271
TitleCryoEM Structure of Zaire Ebola Virus Envelope Glycoprotein GP
Map data
Sample
  • Complex: Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 foldon attached to stabilize soluble trimer
    • Protein or peptide: GP2
    • Protein or peptide: Envelope glycoprotein,GP1
KeywordsEBOV / Ebola / GP / Zaire / Mayinga / MDT-000759 / VIRUS / VIRAL PROTEIN
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, 1976
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsWeidle C / Borst AJ
Funding support United States, 1 items
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 SP / Fiala B / Ravichandran R / Carr KD / Zak SE / Zumbrun EE / Murphy M / Chan S / Skotheim R / Borst AJ / Lauren C / Correnti CE / Dye JM / Baker D / King NP / Stewart LJ
History
DepositionDec 11, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48271.png

Downloads & links

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Map

FileDownload / File: emd_48271.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0213
Minimum - Maximum-0.0018713884 - 2.1447322
Average (Standard dev.)0.0017808846 (±0.031518158)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #7

Fileemd_48271_additional_1.map
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Additional map: #6

Fileemd_48271_additional_2.map
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Additional map: #5

Fileemd_48271_additional_3.map
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Additional map: #4

Fileemd_48271_additional_4.map
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Additional map: #3

Fileemd_48271_additional_5.map
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Additional map: #2

Fileemd_48271_additional_6.map
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Additional map: #1

Fileemd_48271_additional_7.map
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Half map: #2

Fileemd_48271_half_map_1.map
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Half map: #1

Fileemd_48271_half_map_2.map
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Sample components

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Entire : Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 f...

EntireName: Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 foldon attached to stabilize soluble trimer
Components
  • Complex: Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 foldon attached to stabilize soluble trimer
    • Protein or peptide: GP2
    • Protein or peptide: Envelope glycoprotein,GP1

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Supramolecule #1: Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 f...

SupramoleculeName: Ebola GP trimer. Furin Cleaved to form GP1 and GP2 subunits, T4 foldon attached to stabilize soluble trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Molecular weightTheoretical: 162.507 KDa

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Macromolecule #1: GP2

MacromoleculeName: GP2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Molecular weightTheoretical: 18.989391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EAIVNAQPKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYIEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDGSGYIPEA PRDGQAYVRK DGEWVLLSTF L GTHHHHHH

UniProtKB: Envelope glycoprotein

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Macromolecule #2: Envelope glycoprotein,GP1

MacromoleculeName: Envelope glycoprotein,GP1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Molecular weightTheoretical: 35.406648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSSIPLGVIH NSALQVSDVD KLVCRDKLSS TNQLRSVGLN LEGNGVATDV PSATKRWGFR SGVPPKVVNY EAGEWAENCY NLEIKKPDG SECLPAAPDG IRGFPRCRYV HKVSGTGPCA GDFAFHKEGA FFLYDRLAST VIYRGTTFAE GVVAFLILPQ A KKDFFSSH ...String:
GSSIPLGVIH NSALQVSDVD KLVCRDKLSS TNQLRSVGLN LEGNGVATDV PSATKRWGFR SGVPPKVVNY EAGEWAENCY NLEIKKPDG SECLPAAPDG IRGFPRCRYV HKVSGTGPCA GDFAFHKEGA FFLYDRLAST VIYRGTTFAE GVVAFLILPQ A KKDFFSSH PLREPVNATE DPSSGYYSTT IRYQATGFGT NETEYLFEVD NLTYVQLESR FTPQFLLQLN ETIYTSGKRS NT TGKLIWK VNPEIDTTIG EWAFWETKKN LTRKIRSEEL SFTVVSTHHQ DTGEESASSG KLGLITNTIA GVAGLITGGR RTR R

UniProtKB: Envelope glycoprotein, Envelope glycoprotein

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMtris(hydroxymethyl)aminomethane
300.0 mMSodium ChlorideNaCl

Details: 20mM Tris pH 7.5 300mM NaCl
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 30 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 39.0 kPa / Details: 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details20mM Tris pH 7.5, 300mM NaCl

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3128 / Average exposure time: 5.0 sec. / Average electron dose: 56.69 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 540665
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab Initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Non Uniform Refinement / Number images used: 189700
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 16 / Avg.num./class: 11907 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5jq3


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsCrystal Structure 5JQ3 was used as a starting model and fit with Chimera. Structure was further refined in Coot, Phenix, ChimeraX, Isolde
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

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

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