[English] 日本語
Yorodumi
- PDB-6jjd: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jjd
TitleCryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP
ComponentsCapsid proteinCapsid
KeywordsVIRUS LIKE PARTICLE / Giant freshwater prawn Macrobrachium rosenbergii / T=3 icosahedral particle / Double-stranded RNA virus / Canonical jelly-roll beta-barrel fold
Function / homologyViral coat protein subunit / Capsid protein alpha
Function and homology information
Biological speciesMacrobrachium rosenbergii nodavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsChang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y.
Funding support Taiwan, 8items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)MOST 103-2321-B-001-048 Taiwan
Ministry of Science and Technology (Taiwan)MOST 104-2321-B-001-019 Taiwan
Ministry of Science and Technology (Taiwan)MOST 105-2321-B-001-009 Taiwan
Ministry of Science and Technology (Taiwan)MOST 106-0210-01-15-02 Taiwan
Ministry of Science and Technology (Taiwan)MOST 106-0210-01-15-04 Taiwan
Ministry of Science and Technology (Taiwan)MOST 107-0210-01-19-01 Taiwan
Ministry of Science and Technology (Taiwan)MOST 107-0210-01-19-02 Taiwan
Academia Sinica (Taiwan)AS-103-TP-B12 Taiwan
CitationJournal: To Be Published
Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) full VLP
Authors: Chang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y.
History
DepositionFeb 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-9707
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9707
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,72210
Polymers124,4423
Non-polymers2817
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,483,348600
Polymers7,466,515180
Non-polymers16,833420
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 624 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)623,61250
Polymers622,21015
Non-polymers1,40335
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 748 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)748,33560
Polymers746,65218
Non-polymers1,68342
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein Capsid protein / Capsid


Mass: 41480.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macrobrachium rosenbergii nodavirus / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15BP6
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: VirusesVirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 7.452 MDa / Experimental value: NO
Source (natural)Organism: Viruses
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pETDuet-1
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Macrobrachium rosenbergii / Strain: Taiwan strain
Virus shellName: capsid proteinCapsid / Diameter: 400 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMSodium chlorideNaClSodium chloride1
250 mMTrisTris1
31 mMCalcium chlorideCaCl21
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 120000 X / Calibrated defocus min: 330 nm / Calibrated defocus max: 3370 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 37 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 1353
Image scansWidth: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategory
2EPU1.11.1.50RELimage acquisition
4RELION2CTF correction
7UCSF Chimera1.11.2model fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX3374model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 8856
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8856 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

+
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