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- PDB-4btq: Coordinates of the bacteriophage phi6 capsid subunits fitted into... -

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Entry
Database: PDB / ID: 4btq
TitleCoordinates of the bacteriophage phi6 capsid subunits fitted into the cryoEM map EMD-1206
ComponentsMAJOR INNER PROTEIN P1
KeywordsVIRAL PROTEIN / CYSTOVIRIDAE / PROCAPSID STRUCTURE / FLEXIBLE FITTING
Function / homology: / Major inner capsid protein P1 / T=2 icosahedral viral capsid / viral inner capsid / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1
Function and homology information
Biological speciesPSEUDOMONAS PHAGE PHI6 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsNemecek, D. / Boura, E. / Wu, W. / Cheng, N. / Plevka, P. / Qiao, J. / Mindich, L. / Heymann, J.B. / Hurley, J.H. / Steven, A.C.
CitationJournal: Structure / Year: 2013
Title: Subunit folds and maturation pathway of a dsRNA virus capsid.
Authors: Daniel Nemecek / Evzen Boura / Weimin Wu / Naiqian Cheng / Pavel Plevka / Jian Qiao / Leonard Mindich / J Bernard Heymann / James H Hurley / Alasdair C Steven /
Abstract: The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits ...The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits in its icosahedral capsid, and capsids as compartments for transcription and replication. ϕ6 assembles as a dodecahedral procapsid that undergoes major conformational changes as it matures into the spherical capsid. We determined the crystal structure of the capsid protein, P1, revealing a flattened trapezoid subunit with an α-helical fold. We also solved the procapsid with cryo-electron microscopy to comparable resolution. Fitting the crystal structure into the procapsid disclosed substantial conformational differences between the two P1 conformers. Maturation via two intermediate states involves remodeling on a similar scale, besides huge rigid-body rotations. The capsid structure and its stepwise maturation that is coupled to sequential packaging of three RNA segments sets the cystoviruses apart from other dsRNA viruses as a dynamic molecular machine.
History
DepositionJun 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: em_image_scans
Revision 1.2Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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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-1206
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  • Superimposition on EM map
  • EMDB-1206
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Assembly

Deposited unit
A: MAJOR INNER PROTEIN P1
B: MAJOR INNER PROTEIN P1


Theoretical massNumber of molelcules
Total (without water)168,3272
Polymers168,3272
Non-polymers00
Water00
1
A: MAJOR INNER PROTEIN P1
B: MAJOR INNER PROTEIN P1
x 60


Theoretical massNumber of molelcules
Total (without water)10,099,641120
Polymers10,099,641120
Non-polymers00
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: MAJOR INNER PROTEIN P1
B: MAJOR INNER PROTEIN P1
x 5


  • icosahedral pentamer
  • 842 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)841,63710
Polymers841,63710
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: MAJOR INNER PROTEIN P1
B: MAJOR INNER PROTEIN P1
x 6


  • icosahedral 23 hexamer
  • 1.01 MDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)1,009,96412
Polymers1,009,96412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, 0.309, 0.809), (0.309, 0.809, -0.5), (-0.809, 0.5, 0.309)
3generate(0.5, -0.309, 0.809), (-0.309, 0.809, 0.5), (-0.809, -0.5, 0.309)
4generate(0.309, 0.809, 0.5), (-0.809, 0.5, -0.309), (-0.5, -0.309, 0.809)
5generate(0.309, -0.809, 0.5), (0.809, 0.5, 0.309), (-0.5, 0.309, 0.809)
6generate(0.809, 0.5, -0.309), (-0.5, 0.309, -0.809), (-0.309, 0.809, 0.5)
7generate(0.809, 0.5, 0.309), (-0.5, 0.309, 0.809), (0.309, -0.809, 0.5)
8generate(0.809, -0.5, -0.309), (0.5, 0.309, 0.809), (-0.309, -0.809, 0.5)
9generate(0.809, -0.5, 0.309), (0.5, 0.309, -0.809), (0.309, 0.809, 0.5)
10generate(0.309, 0.809, -0.5), (-0.809, 0.5, 0.309), (0.5, 0.309, 0.809)
11generate(0.309, -0.809, -0.5), (0.809, 0.5, -0.309), (0.5, -0.309, 0.809)
12generate(0.5, -0.309, -0.809), (-0.309, 0.809, -0.5), (0.809, 0.5, 0.309)
13generate(0.5, 0.309, -0.809), (0.309, 0.809, 0.5), (0.809, -0.5, 0.309)
14generate(-0.5, 0.3089, 0.809), (-0.3089, 0.8091, -0.4999), (-0.809, -0.4999, -0.3091)
15generate(-0.5, -0.3089, 0.809), (0.3089, 0.8091, 0.4999), (-0.809, 0.4999, -0.3091)
16generate(0.0001, 1, -0.0001), (-0.0001, -0.0001, -1), (-1, 0.0001, 0.0001)
17generate(0.0001, 0.0001, 1), (-1, -0.0001, 0.0001), (0.0001, -1, 0.0001)
18generate(-1), (1), (-1)
19generate(1), (1), (1)
20generate(0.809, 0.4999, 0.309), (0.5, -0.3091, -0.809), (-0.3089, 0.809, -0.5)
21generate(0.809, -0.5, 0.3091), (-0.5001, -0.309, 0.809), (-0.309, -0.8091, -0.5)
22generate(-0.309, 0.809, -0.5), (-0.8091, -0.5, -0.3089), (-0.4999, 0.309, 0.8091)
23generate(-0.309, 0.8091, 0.4999), (-0.809, -0.5, 0.309), (0.5, -0.309, 0.8091)
24generate(-0.309, -0.809, -0.5), (0.8091, -0.5, 0.3089), (-0.4999, -0.309, 0.8091)
25generate(-0.309, -0.8091, 0.4999), (0.809, -0.5, -0.309), (0.5, 0.309, 0.8091)
26generate(0.809, -0.5, -0.3089), (-0.5, -0.3091, -0.809), (0.309, 0.809, -0.5001)
27generate(0.8091, 0.4999, -0.309), (0.5, -0.309, 0.809), (0.3089, -0.8091, -0.5)
28generate(-1), (-1, -0.0001), (-0.0001, 1)
29generate(1, -0.0001), (0.0001, 0.0001, 1), (1, -0.0001)
30generate(0.0001, -0.0001, -1), (1, -0.0001, 0.0001), (-0.0001, -1, 0.0001)
31generate(0.0001, -1, 0.0001), (0.0001, -0.0001, -1), (1, 0.0001, 0.0001)
32generate(-0.5, 0.3089, -0.809), (-0.3089, 0.8091, 0.4999), (0.809, 0.4999, -0.3091)
33generate(-0.5, -0.3089, -0.809), (0.3089, 0.8091, -0.4999), (0.809, -0.4999, -0.3091)
34generate(-0.3089, 0.8091, 0.5), (0.8091, 0.4999, -0.309), (-0.5, 0.309, -0.809)
35generate(-0.3089, -0.8091, 0.5), (-0.8091, 0.4999, 0.309), (-0.5, -0.309, -0.809)
36generate(-0.809, 0.5, 0.309), (-0.5, -0.3089, -0.8091), (-0.309, -0.8091, 0.4999)
37generate(-0.809, -0.5, 0.309), (0.5, -0.3089, 0.8091), (-0.309, 0.8091, 0.4999)
38generate(0.4999, 0.309, -0.8091), (-0.309, -0.809, -0.5), (-0.8091, 0.5, -0.3089)
39generate(0.4999, 0.309, 0.8091), (-0.309, -0.809, 0.5), (0.8091, -0.5, -0.3089)
40generate(0.4999, -0.309, -0.8091), (0.309, -0.809, 0.5), (-0.8091, -0.5, -0.3089)
41generate(0.4999, -0.309, 0.8091), (0.309, -0.809, -0.5), (0.8091, 0.5, -0.3089)
42generate(-0.809, 0.5, -0.309), (-0.5, -0.3089, 0.8091), (0.309, 0.8091, 0.4999)
43generate(-0.809, -0.5, -0.309), (0.5, -0.3089, -0.8091), (0.309, -0.8091, 0.4999)
44generate(-0.3089, -0.8091, -0.5), (-0.8091, 0.4999, -0.309), (0.5, 0.309, -0.809)
45generate(-0.3089, 0.8091, -0.5), (0.8091, 0.4999, 0.309), (0.5, -0.309, -0.809)
46generate(-1, 0.0001), (0.0001, 1, 0.0002), (0.0002, -1)
47generate(-0.809, 0.5, -0.309), (0.5, 0.3089, -0.8091), (-0.3091, -0.809, -0.4999)
48generate(-0.8091, -0.5, 0.3089), (-0.5, 0.3091, -0.809), (0.309, -0.809, -0.5001)
49generate(-0.809, -0.5001, -0.309), (-0.5, 0.3089, 0.8091), (-0.3091, 0.809, -0.5)
50generate(-0.8091, 0.5, 0.309), (0.5, 0.3091, 0.809), (0.309, 0.809, -0.5001)
51generate(0.309, 0.809, -0.5), (0.809, -0.5, -0.309), (-0.5, -0.309, -0.809)
52generate(0.3091, -0.8089, 0.5001), (-0.809, -0.5001, -0.309), (0.5, -0.309, -0.809)
53generate(0.309, -0.809, -0.5), (-0.809, -0.5, 0.309), (-0.5, 0.309, -0.809)
54generate(0.309, 0.809, 0.5), (0.809, -0.5, 0.309), (0.5, 0.309, -0.809)
55generate(-0.5, 0.309, -0.809), (0.309, -0.809, -0.5), (-0.809, -0.5, 0.309)
56generate(-0.5, -0.309, 0.809), (-0.309, -0.809, -0.5), (0.809, -0.5, 0.309)
57generate(-0.5, -0.309, -0.809), (-0.309, -0.809, 0.5), (-0.809, 0.5, 0.309)
58generate(-0.5, 0.309, 0.809), (0.309, -0.809, 0.5), (0.809, 0.5, 0.309)
59generate(1, -0.0001, 0.0001), (-0.0001, -1), (0.0001, -1)
60generate(-1, 0.0001), (-1, 0.0001), (0.0001, 0.0001, 1)

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Components

#1: Protein MAJOR INNER PROTEIN P1 / CAPSID SUBUNIT OF THE BACTERIOPHAGE PHI6


Mass: 84163.672 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-761 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS PHAGE PHI6 (virus) / References: UniProt: P11126

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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: BACTERIOPHAGE PHI6 NUCLEOCAPSID / Type: VIRUS / Details: SEE EMDB MAP EMD-1206
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Details: SEE EMDB MAP EMD-1206
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 400 nm
Image recordingFilm or detector model: KODAK SO-163 FILM

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Processing

EM softwareName: P3DR / Category: 3D reconstruction
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 7.5 Å / Num. of particles: 10463
Details: SEE EMDB MAP EMD-1206. FLEXIBLE FIT OF THE CRYSTAL STRUCTURE 4K7H INTO THE CRYOEM MAP EMD-1206.
Symmetry type: POINT
Atomic model buildingPDB-ID: 4K7H

4k7h


Accession code: 4K7H / Source name: PDB / Type: experimental model
RefinementHighest resolution: 7.5 Å
Refinement stepCycle: LAST / Highest resolution: 7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 0 0 6086

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