[English] 日本語
Yorodumi
- EMDB-8769: Negative stain of influenza B virus recombinant neuraminidase bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8769
TitleNegative stain of influenza B virus recombinant neuraminidase bound to 4F11 Fab
Map dataInfluenza B virus bound to 4F11 Fab
Sample
  • Complex: Influenza B neuraminidase bound to 4F11 Fab
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza B virus (B/Malaysia/2506/2004)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsPodolsky K / Subramaniam S
CitationJournal: Nat Microbiol / Year: 2017
Title: Broadly protective murine monoclonal antibodies against influenza B virus target highly conserved neuraminidase epitopes.
Authors: Teddy John Wohlbold / Kira A Podolsky / Veronika Chromikova / Ericka Kirkpatrick / Veronica Falconieri / Philip Meade / Fatima Amanat / Jessica Tan / Benjamin R tenOever / Gene S Tan / ...Authors: Teddy John Wohlbold / Kira A Podolsky / Veronika Chromikova / Ericka Kirkpatrick / Veronica Falconieri / Philip Meade / Fatima Amanat / Jessica Tan / Benjamin R tenOever / Gene S Tan / Sriram Subramaniam / Peter Palese / Florian Krammer /
Abstract: A substantial proportion of influenza-related childhood deaths are due to infection with influenza B viruses, which co-circulate in the human population as two antigenically distinct lineages defined ...A substantial proportion of influenza-related childhood deaths are due to infection with influenza B viruses, which co-circulate in the human population as two antigenically distinct lineages defined by the immunodominant receptor binding protein, haemagglutinin. While broadly cross-reactive, protective monoclonal antibodies against the haemagglutinin of influenza B viruses have been described, none targeting the neuraminidase, the second most abundant viral glycoprotein, have been reported. Here, we analyse a panel of five murine anti-neuraminidase monoclonal antibodies that demonstrate broad binding, neuraminidase inhibition, in vitro antibody-dependent cell-mediated cytotoxicity and in vivo protection against influenza B viruses belonging to both haemagglutinin lineages and spanning over 70 years of antigenic drift. Electron microscopic analysis of two neuraminidase-antibody complexes shows that the conserved neuraminidase epitopes are located on the head of the molecule and that they are distinct from the enzymatic active site. In the mouse model, one therapeutic dose of antibody 1F2 was more protective than the current standard of treatment, oseltamivir, given twice daily for six days.
History
DepositionJun 15, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateNov 1, 2017-
Current statusNov 1, 2017Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.185
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.185
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8769.png

Downloads & links

-
Map

FileDownload / File: emd_8769.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInfluenza B virus bound to 4F11 Fab
Voxel sizeX=Y=Z: 1.8 Å
Density
Contour LevelBy AUTHOR: 0.185 / Movie #1: 0.185
Minimum - Maximum-0.094127856 - 0.4171483
Average (Standard dev.)0.0015293339 (±0.020445801)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z540.000540.000540.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0940.4170.002

-
Supplemental data

-
Sample components

-
Entire : Influenza B neuraminidase bound to 4F11 Fab

EntireName: Influenza B neuraminidase bound to 4F11 Fab
Components
  • Complex: Influenza B neuraminidase bound to 4F11 Fab

-
Supramolecule #1: Influenza B neuraminidase bound to 4F11 Fab

SupramoleculeName: Influenza B neuraminidase bound to 4F11 Fab / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza B virus (B/Malaysia/2506/2004)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.3
StainingType: NEGATIVE / Material: Uranyl formate

-
Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 100.0 e/Å2

-
Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 1.4)
Details: The standard Fourier Shell Correlation-based measures for resolution are generally not very reliable for negative stain reconstructions because they tend to overestimate resolution and can ...Details: The standard Fourier Shell Correlation-based measures for resolution are generally not very reliable for negative stain reconstructions because they tend to overestimate resolution and can result in spurious values that depend on data size rather than quality, a feature that is also true for cryo-EM reconstructions (some of these issues are discussed in Subramaniam et al, Curr Opin Str. Biol 41: 194-202 (2016)). In negative stain reconstructions, we therefore use a comparison of the experimentally obtained maps with maps computed from the fitted coordinates over a range of resolutions and use this to estimate resolution conservatively. The computed maps at 20 A and 25 A are easily comparable to an experimentally obtained map, which is why we used 25 A as an estimate for resolution.
Number images used: 13665

+
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