[English] 日本語
Yorodumi
- PDB-7pe1: Cryo-EM structure of BMV-derived VLP expressed in E. coli and ass... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pe1
TitleCryo-EM structure of BMV-derived VLP expressed in E. coli and assembled in the presence of tRNA (tVLP)
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / BMV / brome mosaic virus / capsid proteins
Function / homologyBromovirus coat protein / Bromovirus coat protein / viral capsid / structural molecule activity / Coat protein
Function and homology information
Biological speciesBrome mosaic virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsRuszkowski, M. / Strugala, A. / Indyka, P. / Urbanowicz, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nanoscale / Year: 2022
Title: Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure.
Authors: Milosz Ruszkowski / Aleksander Strugala / Paulina Indyka / Guillaume Tresset / Marek Figlerowicz / Anna Urbanowicz /
Abstract: The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex ...The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features . In this paper, we describe VLPs assembled from the recombinant capsid protein of brome mosaic virus (BMV). The analysis of VLPs was performed by Cryo-EM reconstructions and allowed us to visualize a few classes of VLPs, giving insight into the VLP self-assembly process. Apart from the mature icosahedral VLP practically identical with native virions, we describe putative VLP intermediates displaying non-icosahedral arrangements of capsomers, proposed to occur before the final disorder-order transition stage of icosahedral VLP assembly. Some of the described VLP classes show a lack of protein shell continuity, possibly resulting from too strong interaction with the cargo (in this case tRNA) with the capsid protein. We believe that our results are a useful prerequisite for the rational design of VLPs in the future and lead the way to the effective production of modified VLPs.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _citation.country / _em_3d_fitting_list.accession_code ..._citation.country / _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 / _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-13344
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-13344
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: Coat protein
Q: Coat protein
R: Coat protein
S: Coat protein
T: Coat protein
V: Coat protein
W: Coat protein
X: Coat protein
Y: Coat protein
Z: Coat protein
AA: Coat protein
BA: Coat protein
CA: Coat protein
DA: Coat protein
EA: Coat protein
FA: Coat protein
GA: Coat protein
HA: Coat protein
IA: Coat protein
JA: Coat protein
KA: Coat protein
LA: Coat protein
MA: Coat protein
NA: Coat protein
OA: Coat protein
PA: Coat protein
QA: Coat protein
RA: Coat protein
SA: Coat protein
TA: Coat protein
UA: Coat protein
VA: Coat protein
WA: Coat protein
XA: Coat protein
YA: Coat protein
ZA: Coat protein
AB: Coat protein
BB: Coat protein
CB: Coat protein
DB: Coat protein
EB: Coat protein
FB: Coat protein
GB: Coat protein
HB: Coat protein
IB: Coat protein
JB: Coat protein
KB: Coat protein
LB: Coat protein
MB: Coat protein
NB: Coat protein
OB: Coat protein
PB: Coat protein
QB: Coat protein
RB: Coat protein
SB: Coat protein
TB: Coat protein
UB: Coat protein
VB: Coat protein
WB: Coat protein
XB: Coat protein
YB: Coat protein
ZB: Coat protein
AC: Coat protein
BC: Coat protein
CC: Coat protein
DC: Coat protein
EC: Coat protein
FC: Coat protein
GC: Coat protein
HC: Coat protein
IC: Coat protein
JC: Coat protein
KC: Coat protein
LC: Coat protein
MC: Coat protein
NC: Coat protein
OC: Coat protein
PC: Coat protein
QC: Coat protein
RC: Coat protein
SC: Coat protein
TC: Coat protein
UC: Coat protein
VC: Coat protein
WC: Coat protein
XC: Coat protein
YC: Coat protein
ZC: Coat protein
AD: Coat protein
BD: Coat protein
CD: Coat protein
DD: Coat protein
ED: Coat protein
FD: Coat protein
GD: Coat protein
HD: Coat protein
ID: Coat protein
JD: Coat protein
KD: Coat protein
LD: Coat protein
MD: Coat protein
ND: Coat protein
OD: Coat protein
PD: Coat protein
QD: Coat protein
RD: Coat protein
SD: Coat protein
TD: Coat protein
UD: Coat protein
VD: Coat protein
WD: Coat protein
XD: Coat protein
YD: Coat protein
ZD: Coat protein
AE: Coat protein
BE: Coat protein
CE: Coat protein
DE: Coat protein
EE: Coat protein
FE: Coat protein
GE: Coat protein
HE: Coat protein
IE: Coat protein
JE: Coat protein
KE: Coat protein
LE: Coat protein
ME: Coat protein
NE: Coat protein
OE: Coat protein
PE: Coat protein
QE: Coat protein
RE: Coat protein
SE: Coat protein
TE: Coat protein
UE: Coat protein
VE: Coat protein
WE: Coat protein
XE: Coat protein
YE: Coat protein
ZE: Coat protein
AF: Coat protein
BF: Coat protein
CF: Coat protein
DF: Coat protein
EF: Coat protein
FF: Coat protein
GF: Coat protein
HF: Coat protein
IF: Coat protein
JF: Coat protein
KF: Coat protein
LF: Coat protein
MF: Coat protein
NF: Coat protein
OF: Coat protein
PF: Coat protein
QF: Coat protein
RF: Coat protein
SF: Coat protein
TF: Coat protein
UF: Coat protein
VF: Coat protein
WF: Coat protein
XF: Coat protein
YF: Coat protein


Theoretical massNumber of molelcules
Total (without water)3,702,365180
Polymers3,702,365180
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area773860 Å2
ΔGint-4217 kcal/mol
Surface area1115210 Å2
MethodPISA

-
Components

#1: Protein ...
Coat protein


Mass: 20568.693 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brome mosaic virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QCJ1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Brome mosaic virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Brome mosaic virus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 4.8
Details: 25 mM NaOAc pH 4.8, 5 mM MgCl2, 25 mM NaCl, 10 mM KCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 / Calibrated magnification: 105000 X / Calibrated defocus min: 900 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17955

-
Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3.1initial Euler assignment
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1419349
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24812 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6VOC

6voc


Accession code: 6VOC / Source name: PDB / Type: experimental model

+
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