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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3571 | |||||||||
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Title | dsRNA bacteriophage phi6 nucleocapsid | |||||||||
![]() | dsRNA bacteriophage phi6 nucleocapsid | |||||||||
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![]() | icosahedral virus capsid shell / virus | |||||||||
Function / homology | ![]() T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral procapsid / viral genome packaging / viral inner capsid / viral outer capsid / virion component => GO:0044423 / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase ...T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral procapsid / viral genome packaging / viral inner capsid / viral outer capsid / virion component => GO:0044423 / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / viral nucleocapsid / RNA binding / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Sun Z / El Omari K | |||||||||
![]() | ![]() Title: Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Authors: Zhaoyang Sun / Kamel El Omari / Xiaoyu Sun / Serban L Ilca / Abhay Kotecha / David I Stuart / Minna M Poranen / Juha T Huiskonen / ![]() ![]() Abstract: Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by ...Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 464.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.8 KB | Display | ![]() |
Images | ![]() | 216.1 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 299.2 KB | Display | ![]() |
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Full document | ![]() | 298.3 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5muuMC ![]() 3572C ![]() 3573C ![]() 5muvC ![]() 5muwC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | dsRNA bacteriophage phi6 nucleocapsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Pseudomonas phage phi6
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Pseudomonas phage phi6
Supramolecule | Name: Pseudomonas phage phi6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all Details: The viral envelope was removed by Triton X-114 extraction NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: Outer shell / Diameter: 565.0 Å / T number (triangulation number): 13 |
Virus shell | Shell ID: 2 / Name: Inner shell / Diameter: 500.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Major inner protein P1
Macromolecule | Name: Major inner protein P1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 85.080711 KDa |
Sequence | String: MFNLKVKDLN GSARGLTQAF AIGELKNQLS VGALQLPLQF TRTFSASMTS ELLWEVGKGN IDPVMYARLF FQYAQAGGAL SVDELVNQF TEYHQSTACN PEIWRKLTAY ITGSSNRAIK ADAVGKVPPT AILEQLRTLA PSEHELFHHI TTDFVCHVLS P LGFILPDA ...String: MFNLKVKDLN GSARGLTQAF AIGELKNQLS VGALQLPLQF TRTFSASMTS ELLWEVGKGN IDPVMYARLF FQYAQAGGAL SVDELVNQF TEYHQSTACN PEIWRKLTAY ITGSSNRAIK ADAVGKVPPT AILEQLRTLA PSEHELFHHI TTDFVCHVLS P LGFILPDA AYVYRVGRTA TYPNFYALVD CVRASDLRRM LTALSSVDSK MLQATFKAKG ALAPALISQH LANAATTAFE RS RGNFDAN AVVSSVLTIL GRLWSPSTPK ELDPSARLRN TNGIDQLRSN LALFIAYQDM VKQRGRAEVI FSDEELSSTI IPW FIEAMS EVSPFKLRPI NETTSYIGQT SAIDHMGQPS HVVVYEDWQF AKEITAFTPV KLANNSNQRF LDVEPGISDR MSAT LAPIG NTFAVSAFVK NRTAVYEAVS QRGTVNSNGA EMTLGFPSVV ERDYALDRDP MVAIAALRTG IVDESLEARA SNDLK RSMF NYYAAVMHYA VAHNPEVVVS EHQGVAAEQG SLYLVWNVRT ELRIPVGYNA IEGGSIRTPE PLEAIAYNKP IQPSEV LQA KVLDLANHTT SIHIWPWHEA STEFAYEDAY SVTIRNKRYT AEVKEFELLG LGQRRERVRI LKPTVAHAII QMWYSWF VE DDRTLAAARR TSRDDAEKLA IDGRRMQNAV TLLRKIEMIG TTGIGASAVH LAQSRIVDQM AGRGLIDDSS DLHVGINR H RIRIWAGLAV LQMMGLLSRS EAEALTKVLG DSNALGMVVA TTDIDPSL UniProtKB: Major inner protein P1 |
-Macromolecule #2: Packaging enzyme P4
Macromolecule | Name: Packaging enzyme P4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: nucleoside-triphosphate phosphatase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 35.198426 KDa |
Sequence | String: MPIVVTQAHI DRVGIAADLL DASPVSLQVL GRPTAINTVV IKTYIAAVME LASKQGGSLA GVDIRPSVLL KDTAIFTKPK AKSADVESD VDVLDTGIYS VPGLARKPVT HRWPSEGIYS GVTALMGATG SGKSITLNEK LRPDVLIRWG EVAEAYDELD T AVHISTLD ...String: MPIVVTQAHI DRVGIAADLL DASPVSLQVL GRPTAINTVV IKTYIAAVME LASKQGGSLA GVDIRPSVLL KDTAIFTKPK AKSADVESD VDVLDTGIYS VPGLARKPVT HRWPSEGIYS GVTALMGATG SGKSITLNEK LRPDVLIRWG EVAEAYDELD T AVHISTLD EMLIVCIGLG ALGFNVAVDS VRPLLFRLKG AASAGGIVAV FYSLLTDISN LFTQYDCSVV MVVNPMVDAE KI EYVFGQV MASTVGAILC ADGNVSRTMF RTNKGRIFNG AAPLAADTHM PSMDRPTSMK ALDHTSIASV APLERGSVDT DDR NSAPRR GANFSL UniProtKB: Packaging enzyme P4 |
-Macromolecule #3: Major outer capsid protein
Macromolecule | Name: Major outer capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 16.018418 KDa |
Sequence | String: MLLPVVARAA VPAIESAIAA TPGLVSRIAA AIGSKVSPSA ILAAVKSNPV VAGLTLAQIG STGYDAYQQL LENHPEVAEM LKDLSFKAD EIQPDFIGNL GQYREELELV EDAARFVGGM SNLIRLRQAL ELDIKYYGLK MQLNDMGYRS UniProtKB: Major outer capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.2 |
Grid | Model: C-flat / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80.0 K / Max: 120.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-22 / Number real images: 900 / Average exposure time: 0.2 sec. / Average electron dose: 0.73 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.3 µm / Nominal magnification: 160000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 1-760 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B main-chains and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-5muu: |
-Atomic model buiding 2
Details | The structure of P8 (L3 to Y147) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints. |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL |
Output model | ![]() PDB-5muu: |
-Atomic model buiding 3
Details | The structure of P4 C-terminus (R292 to L332) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints. |
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Refinement | Protocol: AB INITIO MODEL |
Output model | ![]() PDB-5muu: |