[English] 日本語
Yorodumi
- EMDB-2056: Electron cryo-microscopy of the Hantaan virus glycoprotein spike -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2056
TitleElectron cryo-microscopy of the Hantaan virus glycoprotein spike
Map dataReconstruction of the Hantaan virus Gn-Gc glycoprotein spike complex
Sample
  • Sample: Hantaan virus Gn-Gc glycoprotein spike complex
  • Virus: Hantaan virus
Keywordsglycoprotein complex / viral membrane / fusion
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / membrane
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan virus
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsBattisti AJ / Chu YK / Chipman PR / Kaufmann B / Jonsson CB / Rossmann MG
CitationJournal: J Virol / Year: 2011
Title: Structural studies of Hantaan virus.
Authors: Anthony J Battisti / Yong-Kyu Chu / Paul R Chipman / Bärbel Kaufmann / Colleen B Jonsson / Michael G Rossmann /
Abstract: Hantaan virus is the prototypic member of the Hantavirus genus within the family Bunyaviridae and is a causative agent of the potentially fatal hemorrhagic fever with renal syndrome. The Bunyaviridae ...Hantaan virus is the prototypic member of the Hantavirus genus within the family Bunyaviridae and is a causative agent of the potentially fatal hemorrhagic fever with renal syndrome. The Bunyaviridae are a family of negative-sense RNA viruses with three-part segmented genomes. Virions are enveloped and decorated with spikes derived from a pair of glycoproteins (Gn and Gc). Here, we present cryo-electron tomography and single-particle cryo-electron microscopy studies of Hantaan virus virions. We have determined the structure of the tetrameric Gn-Gc spike complex to a resolution of 2.5 nm and show that spikes are ordered in lattices on the virion surface. Large cytoplasmic extensions associated with each Gn-Gc spike also form a lattice on the inner surface of the viral membrane. Rod-shaped ribonucleoprotein complexes are arranged into nearly parallel pairs and triplets within virions. Our results differ from the T=12 icosahedral organization found for some bunyaviruses. However, a comparison of our results with the previous tomographic studies of the nonpathogenic Tula hantavirus indicates a common structural organization for hantaviruses.
History
DepositionMar 20, 2012-
Header (metadata) releaseMar 22, 2012-
Map releaseMar 22, 2012-
UpdateMar 22, 2012-
Current statusMar 22, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2056.tif

Downloads & links

-
Map

FileDownload / File: emd_2056.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the Hantaan virus Gn-Gc glycoprotein spike complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.4 Å/pix.
x 80 pix.
= 432. Å		5.4 Å/pix.
x 80 pix.
= 432. Å		5.4 Å/pix.
x 80 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-7.12656021 - 8.03274822
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-7.1278.033-0.000

-
Supplemental data

-
Sample components

-
Entire : Hantaan virus Gn-Gc glycoprotein spike complex

EntireName: Hantaan virus Gn-Gc glycoprotein spike complex
Components
  • Sample: Hantaan virus Gn-Gc glycoprotein spike complex
  • Virus: Hantaan virus

-
Supramolecule #1000: Hantaan virus Gn-Gc glycoprotein spike complex

SupramoleculeName: Hantaan virus Gn-Gc glycoprotein spike complex / type: sample / ID: 1000 / Oligomeric state: tetramer of Gn-Gc heterodimers / Number unique components: 1
Molecular weightTheoretical: 392 KDa

-
Supramolecule #1: Hantaan virus

SupramoleculeName: Hantaan virus / type: virus / ID: 1
Details: The Gn-Gc spike was reconstructed from projection images of virions.
NCBI-ID: 11599 / Sci species name: Hantaan virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4 / Details: 0.01 M Tris, 0.1 M NaCl, and 0.001 M EDTA
GridDetails: 200 mesh holey carbon copper grids (R 2/2 Quantifoil; Micro Tools GmbH, Jena, Germany)
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Method: Small aliquots (3.5 microliters) of purified Hantaan virus particles were applied to holey carbon grids and vitrified in liquid ethane under BSL-3 conditions

-
Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/ST
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at greater than 100,000 times magnification
DateSep 13, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Digitization - Sampling interval: 15.0 µm / Number real images: 105 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 55600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

-
Image processing

CTF correctionDetails: phase reversals corrected using applyctf in EMAN
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER
Details: The Gn-Gc glycoprotein spike complex was reconstructed from projection images of intact virions. Four-fold symmetry was enforced in the final cycles of reconstruction.
Number images used: 9806
Final angle assignmentDetails: SPIDER: theta 90 degrees, phi 90 degrees, delta theta for VO EA command=2.0
Final two d classificationNumber classes: 412

+
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