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- PDB-6jjc: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbe... -

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Basic information

Entry
Database: PDB / ID: 6jjc
TitleCryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty VLP
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / Giant freshwater prawn Macrobrachium rosenbergii / T=3 icosahedral particle / Double-stranded RNA virus / Canonical jelly-roll beta-barrel fold
Function / homologyvirion component / Viral coat protein subunit / Capsid protein alpha
Function and homology information
Biological speciesMacrobrachium rosenbergii nodavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsChang, W.H. / Wang, C.H. / Lin, H.H. / Lin, S.Y. / Chong, S.C. / Wu, Y.Y.
Funding support Taiwan, 7items
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
CitationJournal: To Be Published
Title: Cryo-EM structure of giant freshwater prawn Macrobrachium rosenbergii nodavirus (MrNV) semi-empty 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_conn_angle / 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_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-9706
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-9706
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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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
Water00
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))

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Components

#1: Protein Capsid protein


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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Viruses / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 7.452 MDa / Experimental value: NO
Source (natural)Organism: Viruses / Strain: Macrobrachium rosenbergii nodavirus (Taiwan strain)
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 protein / Diameter: 400 nm / Triangulation number (T number): 3
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMSodium chlorideNaCl1
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: 274 K

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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 FIELD / Nominal magnification: 120000 X / Calibrated defocus min: 450 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

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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: 19049
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19049 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

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