[English] 日本語
Yorodumi
- PDB-6tik: Hepatitis B virus core shell--virus-like particle with NadA epitope -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tik
TitleHepatitis B virus core shell--virus-like particle with NadA epitope
ComponentsCapsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
KeywordsVIRUS LIKE PARTICLE / Virus-like particle / VLP / antigen / NadA / Neisseria meningitidis / HBV / HBC / factor H binding protein
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / cell outer membrane / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / viral envelope / structural molecule activity / cell surface ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / cell outer membrane / viral penetration into host nucleus / host cell / host cell cytoplasm / symbiont entry into host cell / viral envelope / structural molecule activity / cell surface / DNA binding / RNA binding / membrane
Similarity search - Function
Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Hepatitis core antigen ...Hepatitis B viral capsid (hbcag) fold / Viral capsid, core domain supefamily, Hepatitis B virus / Factor H binding protein, C-terminal / : / : / Factor H binding protein, C-terminal / Factor H binding protein, N-terminal / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Pilin-like / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative adhesin/invasin / Capsid protein / Factor H-binding protein
Similarity search - Component
Biological speciesHepatitis B virus
Neisseria meningitidis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsRoseman, A.M. / Colllins, R.F. / Derrick, J.P.
Funding support United Kingdom, 1items
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.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-10316
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-10316
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
D: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
B: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
A: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein


Theoretical massNumber of molelcules
Total (without water)248,4674
Polymers248,4674
Non-polymers00
Water00
1
C: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
D: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
B: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
A: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein
x 60


Theoretical massNumber of molelcules
Total (without water)14,908,020240
Polymers14,908,020240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

-
Components

#1: Protein
Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding protein / Core antigen / Core protein / HBcAg / p21.5 / Core antigen / Core protein / HBcAg / p21.5 / ...Core antigen / Core protein / HBcAg / p21.5 / Core antigen / Core protein / HBcAg / p21.5 / Lipoprotein / Lipoprotein GNA1870


Mass: 62116.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus NadA - Partially ordered surface displayed domain: extracellular domain of NadA from ...Details: HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).,HBcS-NadA-CFHbp VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).
Source: (gene. exp.) Hepatitis B virus, (gene. exp.) Neisseria meningitidis (bacteria)
Gene: C, c, core, PreC, preC, nadA, gna1870, fhbp / Production host: Escherichia coli (E. coli)
References: UniProt: Q67855, UniProt: D3IRF1, UniProt: Q6QCC2
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: VLP fusion sequence expressed in E.coli. / Type: COMPLEX
Details: HBcS-NadA-CFHbp Fusion protein with linker regions. VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus NadA - Partially ordered surface displayed domain: ...Details: HBcS-NadA-CFHbp Fusion protein with linker regions. VLP fusion sequence expressed in E.coli. HBc - core shell from hepatitis B virus 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).
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 14.9 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Neisseria meningitidis (bacteria)487
21Hepatitis B virus10407
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pET-17b
Buffer solutionpH: 8 / Details: PBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 104167 X / Calibrated magnification: 100719 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 424 nm / Calibrated defocus max: 3840 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 79 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2367
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.13_2998refinement
PHENIX1.13_2998refinement
EM software
IDNameVersionCategoryDetails
1EMAN22.01particle selection
2EPUimage acquisition
4EMAN22.01CTF correctionthen CTF applied by CryoSPARC
7DockEMmodel fittingused for initial model placement
9PHENIXPHENIX.real-space_refinemodel refinementrefined the model to the map, using weighted geometry restraints also
10cryoSPARCv0.65initial Euler assignment
11cryoSPARCv0.65final Euler assignment
12cryoSPARCv0.65classification
13cryoSPARCv0.653D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10119
Details: Initially ~44,000 particles were initially picked and extracted in EMAN. Approx 12,000 were shell fragments or incomplete. Others were intact but lower resolution, so damaged or affected by ...Details: Initially ~44,000 particles were initially picked and extracted in EMAN. Approx 12,000 were shell fragments or incomplete. Others were intact but lower resolution, so damaged or affected by charging, or other issue. After filtering/cleaning by EMAN2 2D classification 10119 particles were taken forwards for initial 3D reconstruction in EMAN2. This set of 10119 was then 2D cleaned by CryoSPARC to give 9145 particles.
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8598 / Symmetry type: POINT
Atomic model buildingB value: 111.33 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation with the map plus geometry
Details: The 4 protein chains from the original T=4 HBV core shell structure solved by X-ray crystallography (Wynne, Leslie, Crowther, 1999), PDB code 1QGT, representing two independently resolved ...Details: The 4 protein chains from the original T=4 HBV core shell structure solved by X-ray crystallography (Wynne, Leslie, Crowther, 1999), PDB code 1QGT, representing two independently resolved dimeric spikes, were docked into the map using DockEM, and visualised in UCSF Chimera. Part of the chains near the tips of the spikes did not fit well to the map. This region of the map, corresponding to the major immune dominant region where the inserted NadA epitope was placed, was poorly resolved. Therefore the model region according to the native sequence between, but not including, Leu76 to Arg82 was deleted from all 4 chains. This model was then refined against the map with the phenix.real_space_refine program, using global minimisation, simulated annealing, B-factor refinement, and without non-crystallographic symmetry (NCS) restraints. Default parameters were used for other constraints. The resulting model was re-refined once using the local_grid_search option, with all other parameters left unchanged.
Atomic model buildingPDB-ID: 1QGT

1qgt


Accession code: 1QGT / Pdb chain residue range: 1-143 / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0084550
ELECTRON MICROSCOPYf_angle_d0.85616222
ELECTRON MICROSCOPYf_chiral_restr0.0517708
ELECTRON MICROSCOPYf_plane_restr0.0066782
ELECTRON MICROSCOPYf_dihedral_angle_d4.5392674

+
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