[English] 日本語
Yorodumi
- EMDB-2692: cryo-EM structure of Woodchuck Hepatitis Virus capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2692
Titlecryo-EM structure of Woodchuck Hepatitis Virus capsid
Map dataCryo-EM 3-D reconstruction of Woodchuck Hepatitis Virus capsid
Sample
  • Sample: Woodchuck Hepatitis Virus core protein (wCp149)
  • Virus: Woodchuck hepatitis virus
KeywordsWoodchuck hepatitis virus / hepatitis B virus / cryo-EM / core protein
Biological speciesWoodchuck hepatitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsKukreja A / Wang Joesph C-Y / Pierson E / Keifer DZ / Dragnea B / Jarrold MF / Zlotnick A
CitationJournal: J Virol / Year: 2014
Title: Structurally similar woodchuck and human hepadnavirus core proteins have distinctly different temperature dependences of assembly.
Authors: Alexander A Kukreja / Joseph C-Y Wang / Elizabeth Pierson / David Z Keifer / Lisa Selzer / Zhenning Tan / Bogdan Dragnea / Martin F Jarrold / Adam Zlotnick /
Abstract: Woodchuck hepatitis virus (WHV), a close relative of human hepatitis B virus (HBV), has been a key model for disease progression and clinical studies. Sequences of the assembly domain of WHV and HBV ...Woodchuck hepatitis virus (WHV), a close relative of human hepatitis B virus (HBV), has been a key model for disease progression and clinical studies. Sequences of the assembly domain of WHV and HBV core proteins (wCp149 and hCp149, respectively) have 65% identity, suggesting similar assembly behaviors. We report a cryo-electron microscopy (cryo-EM) structure of the WHV capsid at nanometer resolution and characterization of wCp149 assembly. At this resolution, the T=4 capsid structures of WHV and HBV are practically identical. In contrast to their structural similarity, wCp149 demonstrates enhanced assembly kinetics and stronger dimer-dimer interactions than hCp149: at 23 °C and at 100 mM ionic strength, the pseudocritical concentrations of assembly of wCp149 and hCp149 are 1.8 μM and 43.3 μM, respectively. Transmission electron microscopy reveals that wCp149 assembles into predominantly T=4 capsids with a sizeable population of larger, nonicosahedral structures. Charge detection mass spectrometry indicates that T=3 particles are extremely rare compared to the ∼ 5% observed in hCp149 reactions. Unlike hCp149, wCp149 capsid assembly is favorable over a temperature range of 4 °C to 37 °C; van't Hoff analyses relate the differences in temperature dependence to the high positive values for heat capacity, enthalpy, and entropy of wCp149 assembly. Because the final capsids are so similar, these findings suggest that free wCp149 and hCp149 undergo different structural transitions leading to assembly. The difference in the temperature dependence of wCp149 assembly may be related to the temperature range of its hibernating host.
IMPORTANCE: In this paper, we present a cryo-EM structure of a WHV capsid showing its similarity to HBV. We then observe that the assembly properties of the two homologous proteins are very different. ...IMPORTANCE: In this paper, we present a cryo-EM structure of a WHV capsid showing its similarity to HBV. We then observe that the assembly properties of the two homologous proteins are very different. Unlike human HBV, the capsid protein of WHV has evolved to function in a nonhomeostatic environment. These studies yield insight into the interplay between core protein self-assembly and the host environment, which may be particularly relevant to plant viruses and viruses with zoonotic cycles involving insect vectors.
History
DepositionJun 24, 2014-
Header (metadata) releaseJul 9, 2014-
Map releaseNov 19, 2014-
UpdateDec 3, 2014-
Current statusDec 3, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.063
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.063
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2692.png

emd_2692.png

Downloads & links

-
Map

FileDownload / File: emd_2692.map.gz / Format: CCP4 / Size: 101.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM 3-D reconstruction of Woodchuck Hepatitis Virus capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 301 pix.
= 446.684 Å		1.48 Å/pix.
x 301 pix.
= 446.684 Å		1.48 Å/pix.
x 301 pix.
= 446.684 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.484 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.063 / Movie #1: 0.063
Minimum - Maximum-0.09766106 - 0.24926583
Average (Standard dev.)0.00249827 (±0.03142017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions301301301
Spacing301301301
CellA=B=C: 446.684 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4841.4841.484
M x/y/z301301301
origin x/y/z0.0000.0000.000
length x/y/z446.684446.684446.684
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS301301301
D min/max/mean-0.0980.2490.002

-
Supplemental data

-
Sample components

-
Entire : Woodchuck Hepatitis Virus core protein (wCp149)

EntireName: Woodchuck Hepatitis Virus core protein (wCp149)
Components
  • Sample: Woodchuck Hepatitis Virus core protein (wCp149)
  • Virus: Woodchuck hepatitis virus

-
Supramolecule #1000: Woodchuck Hepatitis Virus core protein (wCp149)

SupramoleculeName: Woodchuck Hepatitis Virus core protein (wCp149) / type: sample / ID: 1000 / Oligomeric state: icosahedron / Number unique components: 1
Molecular weightTheoretical: 4.1 MDa

-
Supramolecule #1: Woodchuck hepatitis virus

SupramoleculeName: Woodchuck hepatitis virus / type: virus / ID: 1
Details: WHV is an enveloped virus, but we present the truncated capsid structure here
NCBI-ID: 35269 / Sci species name: Woodchuck hepatitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Marmota monax (woodchuck) / synonym: VERTEBRATES
Host systemOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant cell: E. coli cells / Recombinant plasmid: pET11c
Molecular weightExperimental: 4.1 MDa / Theoretical: 4.1 MDa
Virus shellShell ID: 1 / Name: capsid / T number (triangulation number): 4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 50 mM NaCl, 10 mM HEPES
GridDetails: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 4 seconds before plunging

-
Electron microscopy

MicroscopeJEOL 3200FS
TemperatureAverage: 97.15 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsParallel weak beam illumination
DateDec 6, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 1.484 µm / Number real images: 133 / Average electron dose: 25 e/Å2 / Camera length: 250 / Details: Image is recorded on CCD
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.1 mm / Nominal defocus max: 0.0033 µm / Nominal defocus min: 0.0011 µm / Nominal magnification: 80000
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

DetailsParticles were boxed using e2boxer.py, defocus level was measured by CTFFIND3 and image processing was done by AUTO3DEM
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: OTHER / Software - Name: AUTO3DEM / Number images used: 2254
Final angle assignmentDetails: AUTO3DEM delta angle 0.7

-
Atomic model buiding 1

Initial modelPDB ID:

1qgt


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: Chimera
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