[English] 日本語
Yorodumi
- EMDB-4520: EM structure of a EBOV-GP bound to 3T0331 neutralizing antibody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4520
TitleEM structure of a EBOV-GP bound to 3T0331 neutralizing antibody
Map dataLocal filtered map
Sample
  • Complex: EBOV-GP in complex with neutralizing 3T0331 antibody
    • Complex: EBOV-GP
      • Protein or peptide: Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1
      • Protein or peptide: Envelope glycoprotein
    • Complex: neutralizing 3T0331 antibody
      • Protein or peptide: Light chain
      • Protein or peptide: Heavy chain
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / immune response / viral infection / EBOV / VIRAL PROTEIN
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 speciesEbola virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDiskin R / Cohen-Dvashi H
CitationJournal: Nat Med / Year: 2019
Title: Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV.
Authors: Stefanie A Ehrhardt / Matthias Zehner / Verena Krähling / Hadas Cohen-Dvashi / Christoph Kreer / Nadav Elad / Henning Gruell / Meryem S Ercanoglu / Philipp Schommers / Lutz Gieselmann / ...Authors: Stefanie A Ehrhardt / Matthias Zehner / Verena Krähling / Hadas Cohen-Dvashi / Christoph Kreer / Nadav Elad / Henning Gruell / Meryem S Ercanoglu / Philipp Schommers / Lutz Gieselmann / Ralf Eggeling / Christine Dahlke / Timo Wolf / Nico Pfeifer / Marylyn M Addo / Ron Diskin / Stephan Becker / Florian Klein /
Abstract: Recombinant vesicular stomatitis virus-Zaire Ebola virus (rVSV-ZEBOV) is the most advanced Ebola virus vaccine candidate and is currently being used to combat the outbreak of Ebola virus disease (EVD) ...Recombinant vesicular stomatitis virus-Zaire Ebola virus (rVSV-ZEBOV) is the most advanced Ebola virus vaccine candidate and is currently being used to combat the outbreak of Ebola virus disease (EVD) in the Democratic Republic of the Congo (DRC). Here we examine the humoral immune response in a subset of human volunteers enrolled in a phase 1 rVSV-ZEBOV vaccination trial by performing comprehensive single B cell and electron microscopy structure analyses. Four studied vaccinees show polyclonal, yet reproducible and convergent B cell responses with shared sequence characteristics. EBOV-targeting antibodies cross-react with other Ebolavirus species, and detailed epitope mapping revealed overlapping target epitopes with antibodies isolated from EVD survivors. Moreover, in all vaccinees, we detected highly potent EBOV-neutralizing antibodies with activities comparable or superior to the monoclonal antibodies currently used in clinical trials. These include antibodies combining the IGHV3-15/IGLV1-40 immunoglobulin gene segments that were identified in all investigated individuals. Our findings will help to evaluate and direct current and future vaccination strategies and offer opportunities for novel EVD therapies.
History
DepositionJan 1, 2019-
Header (metadata) releaseJan 16, 2019-
Map releaseOct 2, 2019-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.108
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.108
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6qd7
  • Surface level: 0.108
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qd7
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4520.png

Downloads & links

-
Map

FileDownload / File: emd_4520.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal filtered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å		0.85 Å/pix.
x 360 pix.
= 306. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.108 / Movie #1: 0.108
Minimum - Maximum-4.6505165 - 6.8730187
Average (Standard dev.)0.0031523444 (±0.10268295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 306.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z306.000306.000306.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-4.6516.8730.003

-
Supplemental data

-
Half map: Half map A

Fileemd_4520_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_4520_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : EBOV-GP in complex with neutralizing 3T0331 antibody

EntireName: EBOV-GP in complex with neutralizing 3T0331 antibody
Components
  • Complex: EBOV-GP in complex with neutralizing 3T0331 antibody
    • Complex: EBOV-GP
      • Protein or peptide: Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1
      • Protein or peptide: Envelope glycoprotein
    • Complex: neutralizing 3T0331 antibody
      • Protein or peptide: Light chain
      • Protein or peptide: Heavy chain
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: EBOV-GP in complex with neutralizing 3T0331 antibody

SupramoleculeName: EBOV-GP in complex with neutralizing 3T0331 antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

-
Supramolecule #2: EBOV-GP

SupramoleculeName: EBOV-GP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Ebola virus

-
Supramolecule #3: neutralizing 3T0331 antibody

SupramoleculeName: neutralizing 3T0331 antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Light chain

MacromoleculeName: Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.310885 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLSPGERAT LSCRASQSVS TYLAWYQHQP GQAPRLLIYE ASNRATGIPA RFSGSGSGTE FTLTISSLEP EDVAVYYCQ QRASWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPAT LSLSPGERAT LSCRASQSVS TYLAWYQHQP GQAPRLLIYE ASNRATGIPA RFSGSGSGTE FTLTISSLEP EDVAVYYCQ QRASWPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #2: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.673553 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLLESGGG LVQPGGSLRL SCEASGFPLR DYAMSWVRQA PGRGLQWVST IGGNDNAANY ADSVKGRFTV SRDNSKSTIY LQMNSLRAE DTALYFCAKS VRLSRPSPFD LWGQGSLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLLESGGG LVQPGGSLRL SCEASGFPLR DYAMSWVRQA PGRGLQWVST IGGNDNAANY ADSVKGRFTV SRDNSKSTIY LQMNSLRAE DTALYFCAKS VRLSRPSPFD LWGQGSLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSC

-
Macromolecule #3: Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1

MacromoleculeName: Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 34.887578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSRSIPLGVI HNSALQVSDV DKLVCRDKLS STNQLRSVGL NLEGNGVATD VPSATKRWGF RSGVPPKVVN YEAGEWAENC YNLEIKKPD GSECLPAAPD GIRGFPRCRY VHKVSGTGPC AGDFAFHKEG AFFLYDRLAS TVIYRGTTFA EGVVAFLILP Q AKKDFFSS ...String:
GSRSIPLGVI HNSALQVSDV DKLVCRDKLS STNQLRSVGL NLEGNGVATD VPSATKRWGF RSGVPPKVVN YEAGEWAENC YNLEIKKPD GSECLPAAPD GIRGFPRCRY VHKVSGTGPC AGDFAFHKEG AFFLYDRLAS TVIYRGTTFA EGVVAFLILP Q AKKDFFSS HPLREPVNAT EDPSSGYYST TIRYQATGFG TNETEYLFEV DNLTYVQLES RFTPQFLLQL NETIYTSGKR SN TTGKLIW KVNPEIDTTI GEWAFWETKK NLTRKIRSEE LSFTVV(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

UniProtKB: Envelope glycoprotein

-
Macromolecule #4: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
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

-
Macromolecule #6: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 27.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 109407
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V2) / Number images used: 109407
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

5jq3

source_name: PDB, initial_model_type: experimental model

6qcu

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6qd7:
EM structure of a EBOV-GP bound to 3T0331 neutralizing antibody

+
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