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- EMDB-8240: EBOV GP in complex with IgG c2G4 and c13C6 Fabs -

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Basic information

Entry
Database: EMDB / ID: 8240
TitleEBOV GP in complex with IgG c2G4 and c13C6 Fabs
Map dataEBOV GP in complex with variable Fab domains of IgGs c2G4 and c13C6
SampleEbola virus trimeric surface glycoprotein in complex with IgG c2G4 and c13C6 Fabs:
(Ebola surface glycoprotein, ...) x 2 / (c2G4 variable Fab domain ...) x 2 / (c13C6 variable Fab domain ...) x 2 / (ligand) x 3
Function / homologyFiloviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane ...Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral entry into host cell / host cell cytoplasm / viral envelope / membrane raft / host cell plasma membrane / virion membrane / integral component of membrane / extracellular region / identical protein binding / Envelope glycoprotein
Function and homology information
SourceZaire ebolavirus (strain Mayinga-76) / Zaire ebolavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsPallesen J / Murin CD / de Val N / Cottrell CA / Hastie KM / Turner HL / Fusco ML / Flyak AI / Zeitlin L / Crowe Jr. JE / Andersen KG / Saphire EO / Ward AB
CitationJournal: Nat Microbiol / Year: 2016
Title: Structures of Ebola virus GP and sGP in complex with therapeutic antibodies.
Authors: Jesper Pallesen / Charles D Murin / Natalia de Val / Christopher A Cottrell / Kathryn M Hastie / Hannah L Turner / Marnie L Fusco / Andrew I Flyak / Larry Zeitlin / James E Crowe / Kristian G Andersen / Erica Ollmann Saphire / Andrew B Ward
Validation ReportPDB-ID: 5kel

SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2016 / Header (metadata) release: Sep 7, 2016 / Map release: Sep 7, 2016 / Last update: Jul 18, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5kel
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8240.map.gz (map file in CCP4 format, 58108 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
244 pix
1.31 Å/pix.
= 319.64 Å
244 pix
1.31 Å/pix.
= 319.64 Å
244 pix
1.31 Å/pix.
= 319.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.044981815 - 0.102471
Average (Standard dev.)0.00002815513 (0.0038259183)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions244244244
Origin0.0.0.
Limit243.243.243.
Spacing244244244
CellA=B=C: 319.63998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z244244244
origin x/y/z0.0000.0000.000
length x/y/z319.640319.640319.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS244244244
D min/max/mean-0.0450.1020.000

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Supplemental data

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Sample components

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Entire Ebola virus trimeric surface glycoprotein in complex with IgG c2G...

EntireName: Ebola virus trimeric surface glycoprotein in complex with IgG c2G4 and c13C6 Fabs
Number of components: 10

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Component #1: protein, Ebola virus trimeric surface glycoprotein in complex wit...

ProteinName: Ebola virus trimeric surface glycoprotein in complex with IgG c2G4 and c13C6 Fabs
Recombinant expression: No
MassExperimental: 540 kDa

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Component #2: protein, Ebola surface glycoprotein, GP1

ProteinName: Ebola surface glycoprotein, GP1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 50.974031 kDa
SourceSpecies: Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76
Source (engineered)Expression System: Drosophila melanogaster (fruit fly)

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Component #3: protein, Ebola surface glycoprotein, GP2

ProteinName: Ebola surface glycoprotein, GP2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 16.137119 kDa
SourceSpecies: Zaire ebolavirus / Strain: Mayinga-76
Source (engineered)Expression System: Drosophila melanogaster (fruit fly)

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Component #4: protein, c2G4 variable Fab domain heavy chain

ProteinName: c2G4 variable Fab domain heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.573105 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Nicotiana benthamiana (plant)

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Component #5: protein, c2G4 variable Fab domain light chain

ProteinName: c2G4 variable Fab domain light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.641884 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Nicotiana benthamiana (plant)

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Component #6: protein, c13C6 variable Fab domain heavy chain

ProteinName: c13C6 variable Fab domain heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 13.169679 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Nicotiana benthamiana (plant)

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Component #7: protein, c13C6 variable Fab domain light chain

ProteinName: c13C6 variable Fab domain light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 11.611877 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Nicotiana benthamiana (plant)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 27 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #10: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 9 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/ml / pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 57 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 77.0 - 77.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2526

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 86000
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: EMRinger / Refinement space: REAL
Details: Model building and refinement were conducted using a combination of software programs. The refinement target was optimizing using the MolProbity score while maintaining a high (good) EMRinger score.
Output model

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