[English] 日本語
Yorodumi
- EMDB-3311: Cryo-EM structure of Ebola GP-Fab100-Fab114 ternary complex at pH 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3311
TitleCryo-EM structure of Ebola GP-Fab100-Fab114 ternary complex at pH 5
Map dataCryo-EM reconstruction of Ebola GP-Fab100-Fab114 ternary complex at pH 5
Sample
  • Sample: Ebola GP binds to Fab Fragments of mAb100 and mAb114
  • Protein or peptide: Ebola virus glycoprotein
  • Protein or peptide: mAb100
  • Protein or peptide: mAb114
KeywordsEbola virus neutralization antibody
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Envelope glycoprotein GP2-like, HR1-HR2 / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsMisasi J / Gilman M / Kanekiyo M / Gui M / Cagigi A / Mulangu S / Corti D / Ledgerwood J / Lanzavecchia A / Cunningham J ...Misasi J / Gilman M / Kanekiyo M / Gui M / Cagigi A / Mulangu S / Corti D / Ledgerwood J / Lanzavecchia A / Cunningham J / Muyembe-Tamfun J / Baxa U / Graham B / Xiang Y / Sullivan N / McLellan J
CitationJournal: Science / Year: 2016
Title: Structural and molecular basis for Ebola virus neutralization by protective human antibodies.
Authors: John Misasi / Morgan S A Gilman / Masaru Kanekiyo / Miao Gui / Alberto Cagigi / Sabue Mulangu / Davide Corti / Julie E Ledgerwood / Antonio Lanzavecchia / James Cunningham / Jean Jacques ...Authors: John Misasi / Morgan S A Gilman / Masaru Kanekiyo / Miao Gui / Alberto Cagigi / Sabue Mulangu / Davide Corti / Julie E Ledgerwood / Antonio Lanzavecchia / James Cunningham / Jean Jacques Muyembe-Tamfun / Ulrich Baxa / Barney S Graham / Ye Xiang / Nancy J Sullivan / Jason S McLellan /
Abstract: Ebola virus causes hemorrhagic fever with a high case fatality rate for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination, protect nonhuman ...Ebola virus causes hemorrhagic fever with a high case fatality rate for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination, protect nonhuman primates against all signs of Ebola virus disease, including viremia. Here, we demonstrate that mAb100 recognizes the base of the Ebola virus glycoprotein (GP) trimer, occludes access to the cathepsin-cleavage loop, and prevents the proteolytic cleavage of GP that is required for virus entry. We show that mAb114 interacts with the glycan cap and inner chalice of GP, remains associated after proteolytic removal of the glycan cap, and inhibits binding of cleaved GP to its receptor. These results define the basis of neutralization for two protective antibodies and may facilitate development of therapies and vaccines.
History
DepositionJan 29, 2016-
Header (metadata) releaseFeb 24, 2016-
Map releaseMar 2, 2016-
UpdateApr 13, 2016-
Current statusApr 13, 2016Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0213
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0213
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3311.jpg

Downloads & links

-
Map

FileDownload / File: emd_3311.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of Ebola GP-Fab100-Fab114 ternary complex at pH 5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0213 / Movie #1: 0.0213
Minimum - Maximum-0.05702131 - 0.09657204
Average (Standard dev.)0.00038889 (±0.00414544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0570.0970.000

-
Supplemental data

-
Sample components

-
Entire : Ebola GP binds to Fab Fragments of mAb100 and mAb114

EntireName: Ebola GP binds to Fab Fragments of mAb100 and mAb114
Components
  • Sample: Ebola GP binds to Fab Fragments of mAb100 and mAb114
  • Protein or peptide: Ebola virus glycoprotein
  • Protein or peptide: mAb100
  • Protein or peptide: mAb114

-
Supramolecule #1000: Ebola GP binds to Fab Fragments of mAb100 and mAb114

SupramoleculeName: Ebola GP binds to Fab Fragments of mAb100 and mAb114 / type: sample / ID: 1000
Oligomeric state: One trimer of Ebola GP binds to three fab fragments of mAb100 and three fab fragments of mAb114
Number unique components: 3
Molecular weightTheoretical: 450 KDa

-
Macromolecule #1: Ebola virus glycoprotein

MacromoleculeName: Ebola virus glycoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: GP / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Zaire ebolavirus / Strain: Mayinga / synonym: Ebola virus
SequenceUniProtKB: Envelope glycoprotein

-
Macromolecule #2: mAb100

MacromoleculeName: mAb100 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293Freestyle cells / Recombinant plasmid: CMV/R type and VRC8400

-
Macromolecule #3: mAb114

MacromoleculeName: mAb114 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293Freestyle cells / Recombinant plasmid: CMV/R type and VRC8400

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 5
VitrificationCryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DateMar 26, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 8793
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more