[English] 日本語
Yorodumi
- EMDB-2046: Cryo-electron microscopy study of hepatitis B virus decorated wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2046
TitleCryo-electron microscopy study of hepatitis B virus decorated with the antibody E1
Map data3D reconstruction of antibody-decorated Hepatitis B T=4 particle
Sample
  • Sample: Antibody E1 to Hepatitis B core antigen
  • Virus: Hepatitis B virus
  • Protein or peptide: Antibody E1
KeywordsHepatitis B / core antigen / ALF / acute liver failure / antibody E1 / monoclonal / conformational epitope / fulminant hepatitis / cryo-EM
Biological speciesHomo sapiens (human) / Hepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsWu W / Chen ZC / Cheng NQ / Watts NR / Stahl SJ / Farci P / Purcell RH / Wingfield PT / Steven AC
CitationJournal: J Struct Biol / Year: 2013
Title: Specificity of an anti-capsid antibody associated with Hepatitis B Virus-related acute liver failure.
Authors: Weimin Wu / Zhaochun Chen / Naiqian Cheng / Norman R Watts / Stephen J Stahl / Patrizia Farci / Robert H Purcell / Paul T Wingfield / Alasdair C Steven /
Abstract: Previously, the livers of patients suffering from acute liver failure (ALF), a potentially fatal syndrome arising from infection by Hepatitis B Virus (HBV), were found to contain massive amounts of ...Previously, the livers of patients suffering from acute liver failure (ALF), a potentially fatal syndrome arising from infection by Hepatitis B Virus (HBV), were found to contain massive amounts of an antibody specific for the core antigen (HBcAg) capsid. We have used cryo-electron microscopy and molecular modeling to define its epitope. HBV capsids are icosahedral shells with 25Å-long dimeric spikes, each a 4-helix bundle, protruding from the contiguous "floor". Of the anti-HBcAg antibodies previously characterized, most bind around the spike tip while one binds to the floor. The ALF-associated antibody binds tangentially to a novel site on the side of the spike. This epitope is conformational. The Fab binds with high affinity to its principal determinants but has lower affinities for quasi-equivalent variants. The highest occupancy site is on one side of a spike, with no detectable binding to the corresponding site on the other side. Binding of one Fab per dimer was also observed by analytical ultracentrifugation. The Fab did not bind to the e-antigen dimer, a non-assembling variant of capsid protein. These findings support the propositions that antibodies with particular specificities may correlate with different clinical expressions of HBV infection and that antibodies directed to particular HBcAg epitopes may be involved in ALF pathogenesis.
History
DepositionMar 2, 2012-
Header (metadata) releaseMar 22, 2012-
Map releaseMar 22, 2012-
UpdateJul 3, 2013-
Current statusJul 3, 2013Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_2046.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of antibody-decorated Hepatitis B T=4 particle
Voxel sizeX=Y=Z: 2.457 Å
Density
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.45940518 - 6.02104616
Average (Standard dev.)-0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 491.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.4572.4572.457
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z491.400491.400491.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-1.4596.021-0.000

-
Supplemental data

-
Sample components

-
Entire : Antibody E1 to Hepatitis B core antigen

EntireName: Antibody E1 to Hepatitis B core antigen
Components
  • Sample: Antibody E1 to Hepatitis B core antigen
  • Virus: Hepatitis B virus
  • Protein or peptide: Antibody E1

-
Supramolecule #1000: Antibody E1 to Hepatitis B core antigen

SupramoleculeName: Antibody E1 to Hepatitis B core antigen / type: sample / ID: 1000
Details: The antibody E1 is derived from two ALF patients. T=4 hepatitis B particle is Cp149.3CA
Oligomeric state: One antibody to one face of the dimer / Number unique components: 1
Molecular weightTheoretical: 4.06 MDa

-
Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

-
Macromolecule #1: Antibody E1

MacromoleculeName: Antibody E1 / type: protein_or_peptide / ID: 1 / Details: Molecular weight is for one copy / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Tissue: Plasma / Cell: B-lyphocytes
Molecular weightTheoretical: 50 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 38 % / Chamber temperature: 100 K / Instrument: OTHER / Method: Manual plunging

-
Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51689 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 0.0018 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 5000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 175,000 magnification
DateJul 1, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 52 / Average electron dose: 20 e/Å2
Details: There are two kinds of particle in each micrograph. T=4 and T=3 Hepatitis B particles.
Bits/pixel: 16

-
Image processing

CTF correctionDetails: Micrograph
Final angle assignmentDetails: EMAN convention
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN,EMAN2 / Number images used: 3787
DetailsEMAN and EMAN2 were applied to solve the structure.

-
Atomic model buiding 1

Initial modelPDB ID:

Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: Chimera,Situs
DetailsProtocol: Rigid body. The PDB structure was manually docked into the reconstruction using Chimera and was automatically fitted using Situs.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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