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- EMDB-8159: Negative stain EM structure of Ebola GP in complex with mAb fab Q314 -

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Basic information

Entry
Database: EMDB / ID: EMD-8159
TitleNegative stain EM structure of Ebola GP in complex with mAb fab Q314
Map dataNone
Sample
  • Complex: Ternary complex of Ebola virus glycoprotein and Fab Q314
    • Complex: Ebola virus glycoprotein
    • Complex: fab Q314
Biological speciesEbola virus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 30.2 Å
AuthorsGui M / Xiang Y / Zhang Q / Zhang L
CitationJournal: Sci Rep / Year: 2016
Title: Potent neutralizing monoclonal antibodies against Ebola virus infection.
Authors: Qi Zhang / Miao Gui / Xuefeng Niu / Shihua He / Ruoke Wang / Yupeng Feng / Andrea Kroeker / Yanan Zuo / Hua Wang / Ying Wang / Jiade Li / Chufang Li / Yi Shi / Xuanling Shi / George F Gao / ...Authors: Qi Zhang / Miao Gui / Xuefeng Niu / Shihua He / Ruoke Wang / Yupeng Feng / Andrea Kroeker / Yanan Zuo / Hua Wang / Ying Wang / Jiade Li / Chufang Li / Yi Shi / Xuanling Shi / George F Gao / Ye Xiang / Xiangguo Qiu / Ling Chen / Linqi Zhang /
Abstract: Ebola virus infections cause a deadly hemorrhagic disease for which no vaccines or therapeutics has received regulatory approval. Here we show isolation of three (Q206, Q314 and Q411) neutralizing ...Ebola virus infections cause a deadly hemorrhagic disease for which no vaccines or therapeutics has received regulatory approval. Here we show isolation of three (Q206, Q314 and Q411) neutralizing monoclonal antibodies (mAbs) against the surface glycoprotein (GP) of Ebola virus identified in West Africa in 2014 through sequential immunization of Chinese rhesus macaques and antigen-specific single B cell sorting. These mAbs demonstrated potent neutralizing activities against both pseudo and live Ebola virus independent of complement. Biochemical, single particle EM, and mutagenesis analysis suggested Q206 and Q411 recognized novel epitopes in the head while Q314 targeted the glycan cap in the GP1 subunit. Q206 and Q411 appeared to influence GP binding to its receptor NPC1. Treatment with these mAbs provided partial but significant protection against disease in a mouse model of Ebola virus infection. These novel mAbs could serve as promising candidates for prophylactic and therapeutic interventions against Ebola virus infection.
History
DepositionApr 22, 2016-
Header (metadata) releaseJun 1, 2016-
Map releaseJun 1, 2016-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8159.png

Downloads & links

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Map

FileDownload / File: emd_8159.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 180 pix.
= 302.4 Å		1.68 Å/pix.
x 180 pix.
= 302.4 Å		1.68 Å/pix.
x 180 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.058775384 - 0.13240886
Average (Standard dev.)0.0005028874 (±0.008019434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0590.1320.001

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Supplemental data

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Sample components

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Entire : Ternary complex of Ebola virus glycoprotein and Fab Q314

EntireName: Ternary complex of Ebola virus glycoprotein and Fab Q314
Components
  • Complex: Ternary complex of Ebola virus glycoprotein and Fab Q314
    • Complex: Ebola virus glycoprotein
    • Complex: fab Q314

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Supramolecule #1: Ternary complex of Ebola virus glycoprotein and Fab Q314

SupramoleculeName: Ternary complex of Ebola virus glycoprotein and Fab Q314
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Ebola virus glycoprotein

SupramoleculeName: Ebola virus glycoprotein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Ebola virus

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Supramolecule #3: fab Q314

SupramoleculeName: fab Q314 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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

Concentration0.02 mg/mL
BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 4127
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: EMAN (ver. 2.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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