[English] 日本語
Yorodumi
- PDB-6d5f: Cryo-EM reconstruction of membrane-enveloped filamentous virus SF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6d5f
TitleCryo-EM reconstruction of membrane-enveloped filamentous virus SFV1 (Sulfolobus filamentous virus 1)
Components
  • (Fimbrial protein) x 2
  • DNA (336-MER)
KeywordsVIRUS / filamentous virus / helical symmetry / membrane enveloped virus
Function / homologyDNA / DNA (> 10) / DNA (> 100)
Function and homology information
Biological speciesSulfolobus filamentous virus 1
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, F. / Osinski, T. / Liu, Y. / Krupovic, M. / Prangishvili, D. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile.
Authors: Ying Liu / Tomasz Osinski / Fengbin Wang / Mart Krupovic / Stefan Schouten / Peter Kasson / David Prangishvili / Edward H Egelman /
Abstract: Different forms of viruses that infect archaea inhabiting extreme environments continue to be discovered at a surprising rate, suggesting that the current sampling of these viruses is sparse. We ...Different forms of viruses that infect archaea inhabiting extreme environments continue to be discovered at a surprising rate, suggesting that the current sampling of these viruses is sparse. We describe here Sulfolobus filamentous virus 1 (SFV1), a membrane-enveloped virus infecting Sulfolobus shibatae. The virus encodes two major coat proteins which display no apparent sequence similarity with each other or with any other proteins in databases. We have used cryo-electron microscopy at 3.7 Å resolution to show that these two proteins form a nearly symmetrical heterodimer, which wraps around A-form DNA, similar to what has been shown for SIRV2 and AFV1, two other archaeal filamentous viruses. The thin (∼ 20 Å) membrane of SFV1 is mainly archaeol, a lipid species that accounts for only 1% of the host lipids. Our results show how relatively conserved structural features can be maintained across evolution by both proteins and lipids that have diverged considerably.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 12, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: em_entity_assembly / em_entity_assembly_naturalsource / entity_src_nat
Item: _em_entity_assembly.name / _em_entity_assembly_naturalsource.ncbi_tax_id ..._em_entity_assembly.name / _em_entity_assembly_naturalsource.ncbi_tax_id / _em_entity_assembly_naturalsource.organism / _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-7797
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7797
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fimbrial protein
B: Fimbrial protein
C: Fimbrial protein
D: Fimbrial protein
E: Fimbrial protein
F: Fimbrial protein
G: Fimbrial protein
H: Fimbrial protein
I: Fimbrial protein
J: Fimbrial protein
K: Fimbrial protein
L: Fimbrial protein
M: Fimbrial protein
N: Fimbrial protein
O: Fimbrial protein
P: Fimbrial protein
Q: Fimbrial protein
R: Fimbrial protein
S: Fimbrial protein
T: Fimbrial protein
U: Fimbrial protein
V: Fimbrial protein
W: Fimbrial protein
X: Fimbrial protein
Y: Fimbrial protein
Z: Fimbrial protein
a: Fimbrial protein
b: Fimbrial protein
c: Fimbrial protein
d: Fimbrial protein
e: Fimbrial protein
f: Fimbrial protein
g: Fimbrial protein
h: Fimbrial protein
i: Fimbrial protein
j: Fimbrial protein
k: Fimbrial protein
l: Fimbrial protein
m: Fimbrial protein
n: Fimbrial protein
o: Fimbrial protein
p: Fimbrial protein
q: Fimbrial protein
r: Fimbrial protein
s: Fimbrial protein
t: Fimbrial protein
u: Fimbrial protein
v: Fimbrial protein
w: Fimbrial protein
x: Fimbrial protein
y: Fimbrial protein
z: Fimbrial protein
1: DNA (336-MER)
2: DNA (336-MER)


Theoretical massNumber of molelcules
Total (without water)1,190,47754
Polymers1,190,47754
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area450390 Å2
ΔGint-2996 kcal/mol
Surface area303120 Å2

-
Components

#1: Protein ...
Fimbrial protein


Mass: 22020.135 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Sulfolobus filamentous virus 1
#2: Protein ...
Fimbrial protein


Mass: 15792.202 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Source: (natural) Sulfolobus filamentous virus 1
#3: DNA chain DNA (336-MER)


Mass: 103678.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus filamentous virus 1

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Sulfolobus filamentous virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sulfolobus filamentous virus 1
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 6 / Details: 20 mM Tris-acetate, 250 mM sodium chloride, pH 6.0
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 90 %

-
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 FIELDBright-field microscopy
Image recordingAverage exposure time: 2 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Details: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2.

-
Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
IDNameCategory
1EMAN2particle selection
2EPUimage acquisition
4GctfCTF correction
7Rosettamodel fitting
12RELION3D reconstruction
13SPIDER3D reconstruction
14Rosettamodel refinement
15PHENIXmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 21.02572 ° / Axial rise/subunit: 2.76412 Å / Axial symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87803 / Symmetry type: HELICAL
RefinementHighest resolution: 3.7 Å

+
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