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- EMDB-6234: Negative stain single particle electron microscopy of Marburg Vir... -

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Basic information

Entry
Database: EMDB / ID: EMD-6234
TitleNegative stain single particle electron microscopy of Marburg Virus Glycoproteins bound to antibodies from a human survivor
Map dataReconstruction of Marburg Virus GPdMuc bound to antibody MR201 from a human survivor
Sample
  • Sample: Fab Fragment of MR201 human IgG1 monoclonal antibody to Marburg Virus GP
  • Protein or peptide: GP, mucin-deleted
  • Protein or peptide: Human Monoclonal Antibody IgG1
KeywordsMarburg Virus / Antibodies / Neutralization / Glycoprotein
Biological speciesMarburg marburgvirus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsFlyak A / Ilinykh PA / Murin CD / Garron T / Shen X / Fusco ML / Hashiguchi T / Bornholdt ZA / Slaughter C / Sapparapu G ...Flyak A / Ilinykh PA / Murin CD / Garron T / Shen X / Fusco ML / Hashiguchi T / Bornholdt ZA / Slaughter C / Sapparapu G / Ksiazek TG / Ward AB / Saphire EO / Bukreyev A / Crowe JE
CitationJournal: Cell / Year: 2015
Title: Mechanism of human antibody-mediated neutralization of Marburg virus.
Authors: Andrew I Flyak / Philipp A Ilinykh / Charles D Murin / Tania Garron / Xiaoli Shen / Marnie L Fusco / Takao Hashiguchi / Zachary A Bornholdt / James C Slaughter / Gopal Sapparapu / Curtis ...Authors: Andrew I Flyak / Philipp A Ilinykh / Charles D Murin / Tania Garron / Xiaoli Shen / Marnie L Fusco / Takao Hashiguchi / Zachary A Bornholdt / James C Slaughter / Gopal Sapparapu / Curtis Klages / Thomas G Ksiazek / Andrew B Ward / Erica Ollmann Saphire / Alexander Bukreyev / James E Crowe /
Abstract: The mechanisms by which neutralizing antibodies inhibit Marburg virus (MARV) are not known. We isolated a panel of neutralizing antibodies from a human MARV survivor that bind to MARV glycoprotein ...The mechanisms by which neutralizing antibodies inhibit Marburg virus (MARV) are not known. We isolated a panel of neutralizing antibodies from a human MARV survivor that bind to MARV glycoprotein (GP) and compete for binding to a single major antigenic site. Remarkably, several of the antibodies also bind to Ebola virus (EBOV) GP. Single-particle EM structures of antibody-GP complexes reveal that all of the neutralizing antibodies bind to MARV GP at or near the predicted region of the receptor-binding site. The presence of the glycan cap or mucin-like domain blocks binding of neutralizing antibodies to EBOV GP, but not to MARV GP. The data suggest that MARV-neutralizing antibodies inhibit virus by binding to infectious virions at the exposed MARV receptor-binding site, revealing a mechanism of filovirus inhibition.
History
DepositionJan 6, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseJul 22, 2015-
UpdateJul 22, 2015-
Current statusJul 22, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.87
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.87
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6234.jpg

Downloads & links

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Map

FileDownload / File: emd_6234.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Marburg Virus GPdMuc bound to antibody MR201 from a human survivor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. Å		4.1 Å/pix.
x 80 pix.
= 328. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.87 / Movie #1: 3.87
Minimum - Maximum-5.61409855 - 18.252414699999999
Average (Standard dev.)0.0 (±0.99999905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 328.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z328.000328.000328.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-5.61418.252-0.000

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Supplemental data

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Sample components

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Entire : Fab Fragment of MR201 human IgG1 monoclonal antibody to Marburg V...

EntireName: Fab Fragment of MR201 human IgG1 monoclonal antibody to Marburg Virus GP
Components
  • Sample: Fab Fragment of MR201 human IgG1 monoclonal antibody to Marburg Virus GP
  • Protein or peptide: GP, mucin-deleted
  • Protein or peptide: Human Monoclonal Antibody IgG1

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Supramolecule #1000: Fab Fragment of MR201 human IgG1 monoclonal antibody to Marburg V...

SupramoleculeName: Fab Fragment of MR201 human IgG1 monoclonal antibody to Marburg Virus GP
type: sample / ID: 1000 / Oligomeric state: trimer / Number unique components: 2
Molecular weightTheoretical: 310 KDa

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Macromolecule #1: GP, mucin-deleted

MacromoleculeName: GP, mucin-deleted / type: protein_or_peptide / ID: 1 / Name.synonym: glycoprotein
Details: Recombinant Marburg Virus GP; mucin-like domains were not included in the construct.
Number of copies: 1 / Oligomeric state: trimer / Recombinant expression: Yes
Source (natural)Organism: Marburg marburgvirus / synonym: Marburg virus
Molecular weightTheoretical: 160 MDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly) / Recombinant cell: Schneider S2 cells / Recombinant plasmid: pMT-puro

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Macromolecule #2: Human Monoclonal Antibody IgG1

MacromoleculeName: Human Monoclonal Antibody IgG1 / type: protein_or_peptide / ID: 2 / Name.synonym: IgG1, monoclonal mAb / Details: Human monoclonal antibody IgG1, MR201 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Blood / Cell: Peripheral blood mononuclear cells
Molecular weightTheoretical: 150 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris, 150 mM NaCl
StainingType: NEGATIVE
Details: Grids with absorbed protein stained with 2% uranyl formate for 30 seconds
GridDetails: 400 mesh copper grid with carbon support, plasma cleaned 20 seconds (Ar/O2 mix, Gatan)
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
DateNov 12, 2013
Image recordingCategory: CCD / Film or detector model: OTHER / Number real images: 275
Electron beamAcceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected using DoG picker.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 12896

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