[English] 日本語
Yorodumi
- PDB-8ugq: CryoEM Structure of Maize Streak Virus (MSV) - Geminivirus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ugq
TitleCryoEM Structure of Maize Streak Virus (MSV) - Geminivirus
Components
  • Capsid protein
  • DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
KeywordsVIRAL PROTEIN / Plant / ssDNA / Icosahedron / capsid
Function / homology
Function and homology information


T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding
Similarity search - Function
Geminivirus MSV 27Kd coat protein / Geminivirus AR1/BR1 coat protein / Geminivirus coat protein/nuclear export factor BR1 family / Viral coat protein subunit
Similarity search - Domain/homology
DNA / Capsid protein
Similarity search - Component
Biological speciesMaize streak virus genotype A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsMcKenna, R. / Bennett, A.B. / Mietzsch, M. / Hull, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF DMS 1563234 United States
CitationJournal: To Be Published
Title: The two states of Maize Streak Virus (MSV) Geminivirus Architecture
Authors: McKenna, R. / Bennett, A.B. / Mietzsch, M. / Hull, J.A.
History
DepositionOct 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
L: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
B: Capsid protein
M: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
C: Capsid protein
N: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
D: Capsid protein
O: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
E: Capsid protein
P: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
F: Capsid protein
Q: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
G: Capsid protein
R: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
H: Capsid protein
S: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
I: Capsid protein
T: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
J: Capsid protein
U: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')
K: Capsid protein
V: DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)325,05322
Polymers325,05322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
Capsid protein / Coat protein / CP


Mass: 26880.529 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maize streak virus genotype A (isolate Nigeria)
Strain: isolate Nigeria / Gene: V1 / Production host: Agrobacterium tumefaciens (bacteria) / References: UniProt: P06448
#2: DNA chain
DNA (5'-D(P*CP*GP*AP*AP*CP*CP*CP*CP*A)-3')


Mass: 2669.778 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maize streak virus genotype A (isolate Nigeria)
Strain: isolate Nigeria / Production host: Agrobacterium tumefaciens (bacteria)

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Maize streak virus - [Nigeria] / Type: VIRUS
Details: Gemini capsid is a Pseudo T=1 icosahedron. The structure contains both protein and ssDNA.
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Maize streak virus genotype A (isolate Nigeria) / Strain: isolate Nigeria
Source (recombinant)Organism: Agrobacterium tumefaciens (bacteria)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Zea mays
Virus shellTriangulation number (T number): 1
Buffer solutionpH: 4
Buffer componentConc.: 0.1 M / Name: Sodium acetate / Formula: NaAc
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3627 nm / Nominal defocus min: 947 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Num. of real images: 1408

-
Processing

EM software
IDNameCategory
2Leginonimage acquisition
7Cootmodel fitting
12cisTEM3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1408 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model buildingType: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009209930
ELECTRON MICROSCOPYf_angle_d0.977289240
ELECTRON MICROSCOPYf_dihedral_angle_d16.451156830
ELECTRON MICROSCOPYf_chiral_restr0.0531570
ELECTRON MICROSCOPYf_plane_restr0.00633800

+
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