[English] 日本語
Yorodumi
- EMDB-10316: Hepatitis B virus core protein virus-like particle displaying the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10316
TitleHepatitis B virus core protein virus-like particle displaying the antigen: extra cellular adhesion domain NadA from Neisseria meningitidis.
Map data
SampleVLP fusion sequence expressed in E.coli.:
HBcS-NadA-CFHbp
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / host cell cytoplasm / viral entry into host cell / viral envelope / pathogenesis / structural molecule activity / RNA binding / DNA binding
Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / YadA-like, C-terminal / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Lipoprotein GNA1870-related, C-terminal
Putative adhesin/invasin / Capsid protein / Factor H-binding protein
Biological speciesNeisseria meningitidis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCollins RF / Roseman AM / Derrick JP
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBRIC PhD, BBSRC Reference BB/K02034X/1 United Kingdom
CitationJournal: Vaccine / Year: 2020
Title: An assessment of the use of Hepatitis B Virus core protein virus-like particles to display heterologous antigens from Neisseria meningitidis.
Authors: Sebastian Aston-Deaville / Emil Carlsson / Muhammad Saleem / Angela Thistlethwaite / Hannah Chan / Sunil Maharjan / Alessandra Facchetti / Ian M Feavers / C Alistair Siebert / Richard F ...Authors: Sebastian Aston-Deaville / Emil Carlsson / Muhammad Saleem / Angela Thistlethwaite / Hannah Chan / Sunil Maharjan / Alessandra Facchetti / Ian M Feavers / C Alistair Siebert / Richard F Collins / Alan Roseman / Jeremy P Derrick /
Abstract: Neisseria meningitidis is the causative agent of meningococcal meningitis and sepsis and remains a significant public health problem in many countries. Efforts to develop a comprehensive vaccine ...Neisseria meningitidis is the causative agent of meningococcal meningitis and sepsis and remains a significant public health problem in many countries. Efforts to develop a comprehensive vaccine against serogroup B meningococci have focused on the use of surface-exposed outer membrane proteins. Here we report the use of virus-like particles derived from the core protein of Hepatitis B Virus, HBc, to incorporate antigen domains derived from Factor H binding protein (FHbp) and the adhesin NadA. The extracellular domain of NadA was inserted into the major immunodominant region of HBc, and the C-terminal domain of FHbp at the C-terminus (CFHbp), creating a single polypeptide chain 3.7-fold larger than native HBc. Remarkably, cryoelectron microscopy revealed that the construct formed assemblies that were able to incorporate both antigens with minimal structural changes to native HBc. Electron density was weak for NadA and absent for CFHbp, partly attributable to domain flexibility. Following immunization of mice, three HBc fusions (CFHbp or NadA alone, NadA + CFHbp) were able to induce production of IgG1, IgG2a and IgG2b antibodies reactive against their respective antigens at dilutions in excess of 1:18,000. However, only HBc fusions containing NadA elicited the production of antibodies with serum bactericidal activity. It is hypothesized that this improved immune response is attributable to the adoption of a more native-like folding of crucial conformational epitopes of NadA within the chimeric VLP. This work demonstrates that HBc can incorporate insertions of large antigen domains but that maintenance of their three-dimensional structure is likely to be critical in obtaining a protective response.
Validation ReportPDB-ID: 6tik

SummaryFull reportAbout validation report
History
DepositionSep 18, 2019-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6tik
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6tik
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_10316.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 512 pix.
= 711.68 Å
1.39 Å/pix.
x 512 pix.
= 711.68 Å
1.39 Å/pix.
x 512 pix.
= 711.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-1.1796018 - 4.9631643
Average (Standard dev.)0.011435016 (±0.23314595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 711.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z711.680711.680711.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.1804.9630.011

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_10316_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: Mask for FSC calculation

Fileemd_10316_additional_2.map
AnnotationMask for FSC calculation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half map A.

Fileemd_10316_half_map_1.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half map B.

Fileemd_10316_half_map_2.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire VLP fusion sequence expressed in E.coli.

EntireName: VLP fusion sequence expressed in E.coli.
Details: HBcS-NadA-CFHbp Fusion protein with linker regions. HBc - Ordered core of VLP: from HBV core protein (NCBI taxonomy ID 10407). NadA - Partially ordered surface displayed domain: ...Details: HBcS-NadA-CFHbp Fusion protein with linker regions. HBc - Ordered core of VLP: from HBV core protein (NCBI taxonomy ID 10407). NadA - Partially ordered surface displayed domain: extracellular domain of NadA from Neisseria meningitidis (NCBI taxonomy ID 487). CFHbp - Unresolved/disordered component : C-terminal domain of factor H binding protein from Neisseria meningitidis (NCBI taxonomy ID 487).
Number of components: 2

-
Component #1: protein, VLP fusion sequence expressed in E.coli.

ProteinName: VLP fusion sequence expressed in E.coli.
Details: HBcS-NadA-CFHbp Fusion protein with linker regions. HBc - Ordered core of VLP: from HBV core protein (NCBI taxonomy ID 10407). NadA - Partially ordered surface displayed domain: ...Details: HBcS-NadA-CFHbp Fusion protein with linker regions. HBc - Ordered core of VLP: from HBV core protein (NCBI taxonomy ID 10407). NadA - Partially ordered surface displayed domain: extracellular domain of NadA from Neisseria meningitidis (NCBI taxonomy ID 487). CFHbp - Unresolved/disordered component : C-terminal domain of factor H binding protein from Neisseria meningitidis (NCBI taxonomy ID 487).
Recombinant expression: No
MassTheoretical: 14.9 MDa
SourceSpecies: Neisseria meningitidis (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET-17b / Strain: BL21

-
Component #2: protein, HBcS-NadA-CFHbp

ProteinName: HBcS-NadA-CFHbp / Details: expressed fusion chimera protein / Recombinant expression: No

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / Buffer solution: PBS / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 90 %
Details: 3 ul applied for 30s at room temperature, then 4-5 s blot..

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 79 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 104167 X (nominal), 100719 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.0 - 2.5 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2367 / Sampling size: 14 µm

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 8598
3D reconstructionSoftware: cryoSPARC / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more

-
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.

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