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- PDB-4btg: Coordinates of the bacteriophage phi6 capsid subunits (P1A and P1... -

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Basic information

Entry
Database: PDB / ID: 4btg
TitleCoordinates of the bacteriophage phi6 capsid subunits (P1A and P1B) fitted into the cryoEM reconstruction of the procapsid at 4.4 A resolution
ComponentsMAJOR INNER PROTEIN P1
KeywordsVIRUS / 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: 4.4 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 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _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
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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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(0.309014, -0.951057), (0.951057, 0.309014), (1)
3generate(-0.80902, -0.587781), (0.587781, -0.80902), (1)
4generate(-0.809012, 0.587793), (-0.587793, -0.809012), (1)
5generate(0.309028, 0.951053), (-0.951053, 0.309028), (1)
6generate(-1, 7.0E-6), (1), (-7.0E-6, -1)
7generate(-0.309014, -0.951057, 2.0E-6), (-0.951057, 0.309014, 7.0E-6), (-7.0E-6, -1)
8generate(0.80902, -0.587781, -6.0E-6), (-0.587781, -0.80902, 4.0E-6), (-7.0E-6, -1)
9generate(0.809012, 0.587793, -6.0E-6), (0.587793, -0.809012, -4.0E-6), (-7.0E-6, -1)
10generate(-0.309028, 0.951053, 2.0E-6), (0.951053, 0.309028, -7.0E-6), (-7.0E-6, -1)
11generate(0.3618, -0.587786, -0.723607), (0.262864, 0.809016, -0.525733), (0.894429, 0.44721)
12generate(-0.138197, -0.951055, 0.276397), (0.425322, -0.309021, -0.850651), (0.894429, 0.44721)
13generate(-0.44721, 7.0E-6, 0.894429), (-3.0E-6, -1, 6.0E-6), (0.894429, 0.44721)
14generate(-0.138191, 0.95106, 0.276385), (-0.425324, -0.309007, 0.850655), (0.894429, 0.44721)
15generate(0.361804, 0.587775, -0.723615), (-0.262859, 0.809025, 0.525722), (0.894429, 0.44721)
16generate(-0.447217, -0.525727, -0.723607), (0.85065, -2.0E-6, -0.525733), (0.276391, -0.850653, 0.44721)
17generate(-0.947213, -0.162456, 0.276397), (-0.162466, -0.499997, -0.850651), (0.276391, -0.850653, 0.44721)
18generate(-0.138187, 0.425325, 0.894429), (-0.951058, -0.309011, 6.0E-6), (0.276391, -0.850653, 0.44721)
19generate(0.861809, 0.425319, 0.276385), (-0.425315, 0.30902, 0.850655), (0.276391, -0.850653, 0.44721)
20generate(0.67081, -0.162466, -0.723615), (0.688202, 0.499994, 0.525722), (0.276391, -0.850653, 0.44721)
21generate(-0.638193, 0.262872, -0.723607), (0.262861, -0.809017, -0.525733), (-0.723611, -0.525728, 0.44721)
22generate(-0.447207, 0.850653, 0.276397), (-0.525731, 9.0E-6, -0.850651), (-0.723611, -0.525728, 0.44721)
23generate(0.361807, 0.262856, 0.894429), (-0.587778, 0.809022, 6.0E-6), (-0.723611, -0.525728, 0.44721)
24generate(0.670814, -0.688201, 0.276385), (0.162467, 0.49999, 0.850655), (-0.723611, -0.525728, 0.44721)
25generate(0.052775, -0.688183, -0.723615), (0.688187, -0.500014, 0.525722), (-0.723611, -0.525728, 0.44721)
26generate(0.052796, 0.68819, -0.723607), (-0.688194, -0.499994, -0.525733), (-0.723603, 0.525738, 0.44721)
27generate(0.670826, 0.688183, 0.276397), (-0.16245, 0.500003, -0.850651), (-0.723603, 0.525738, 0.44721)
28generate(0.361794, -0.262873, 0.894429), (0.587795, 0.80901, 6.0E-6), (-0.723603, 0.525738, 0.44721)
29generate(-0.447227, -0.850646, 0.276385), (0.525724, -1.2E-5, 0.850655), (-0.723603, 0.525738, 0.44721)
30generate(-0.638193, -0.262851, -0.723615), (-0.262883, -0.809017, 0.525722), (-0.723603, 0.525738, 0.44721)
31generate(0.670823, 0.162449, -0.723607), (-0.688185, 0.500006, -0.525733), (0.276403, 0.850649, 0.44721)
32generate(0.861797, -0.425336, 0.276397), (0.425332, 0.309007, -0.850651), (0.276403, 0.850649, 0.44721)
33generate(-0.138207, -0.425319, 0.894429), (0.951052, -0.309031, 6.0E-6), (0.276403, 0.850649, 0.44721)
34generate(-0.947213, 0.162477, 0.276385), (0.162445, -0.499997, 0.850655), (0.276403, 0.850649, 0.44721)
35generate(-0.447197, 0.525734, -0.723615), (-0.850656, 1.9E-5, 0.525722), (0.276403, 0.850649, 0.44721)
36generate(-0.361869, 0.262914, -0.894386), (0.587786, 0.809016), (0.723573, -0.525708, -0.447295)
37generate(-0.670841, -0.688177, -0.276378), (-0.162524, 0.500044, -0.850613), (0.723573, -0.525708, -0.447295)
38generate(-0.05273, -0.688227, 0.723577), (-0.688231, -0.499975, -0.525703), (0.723573, -0.525708, -0.447295)
39generate(0.638253, 0.262833, 0.723569), (-0.262822, -0.809043, 0.525714), (0.723573, -0.525708, -0.447295)
40generate(0.447188, 0.850665, -0.27639), (0.525799, -3.7E-5, 0.850609), (0.723573, -0.525708, -0.447295)
41generate(0.138224, 0.425402, -0.894386), (0.951055, -0.309021), (-0.276384, -0.850611, -0.447295)
42generate(-0.861795, 0.425352, -0.276378), (0.425348, 0.30909, -0.850613), (-0.276384, -0.850611, -0.447295)
43generate(-0.670838, -0.162522, 0.723577), (-0.688178, 0.500048, -0.525703), (-0.276384, -0.850611, -0.447295)
44generate(0.447198, -0.525796, 0.723569), (-0.850662, -4.7E-5, 0.525714), (-0.276384, -0.850611, -0.447295)
45generate(0.947219, -0.162434, -0.27639), (0.162445, -0.500076, 0.850609), (-0.276384, -0.850611, -0.447295)
46generate(0.447295, -3.0E-6, -0.894386), (-7.0E-6, -1), (-0.894386, 6.0E-6, -0.447295)
47generate(0.138227, 0.951056, -0.276378), (0.425401, -0.309017, -0.850613), (-0.894386, 6.0E-6, -0.447295)
48generate(-0.361867, 0.587783, 0.723577), (0.262917, 0.809018, -0.525703), (-0.894386, 6.0E-6, -0.447295)
49generate(-0.361871, -0.58779, 0.723569), (-0.262911, 0.809014, 0.525714), (-0.894386, 6.0E-6, -0.447295)
50generate(0.13822, -0.951054, -0.27639), (-0.425404, -0.309025, 0.850609), (-0.894386, 6.0E-6, -0.447295)
51generate(0.138217, -0.425404, -0.894386), (-0.95106, -0.309007), (-0.276372, 0.850615, -0.447295)
52generate(0.947223, 0.162427, -0.276378), (-0.162438, -0.500072, -0.850613), (-0.276372, 0.850615, -0.447295)
53generate(0.447194, 0.525789, 0.723577), (0.850668, -5.1E-5, -0.525703), (-0.276372, 0.850615, -0.447295)
54generate(-0.670845, 0.162525, 0.723569), (0.688175, 0.50004, 0.525714), (-0.276372, 0.850615, -0.447295)
55generate(-0.861795, -0.425344, -0.27639), (-0.425356, 0.30909, 0.850609), (-0.276372, 0.850615, -0.447295)
56generate(-0.361873, -0.262909, -0.894386), (-0.587775, 0.809025), (0.723581, 0.525698, -0.447295)
57generate(0.447183, -0.850672, -0.276378), (-0.525793, -4.1E-5, -0.850613), (0.723581, 0.525698, -0.447295)
58generate(0.638245, -0.262831, 0.723577), (0.26282, -0.80905, -0.525703), (0.723581, 0.525698, -0.447295)
59generate(-0.05273, 0.688235, 0.723569), (0.688223, -0.499975, 0.525714), (0.723581, 0.525698, -0.447295)
60generate(-0.670834, 0.688179, -0.27639), (0.162521, 0.500051, 0.850609), (0.723581, 0.525698, -0.447295)

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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 genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PHAGE PHI6 (virus) / Plasmid: PLM3572 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / 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: P1247 PHI6 PROCAPSID / Type: VIRUS
Buffer solutionName: 10 MM POTASSIUM PHOSPHATE, 5 MM MGCL2 / pH: 8 / Details: 10 MM POTASSIUM PHOSPHATE, 5 MM MGCL2
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 20, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 46000 X / Calibrated magnification: 44739 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 220
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2MDFFmodel fitting
3UCSF Chimeramodel fitting
4Bsoft3D reconstruction
5EMAN3D reconstruction
CTF correctionDetails: PARTICLES FROM EACH MICROGRAPH
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.4 Å / Num. of particles: 18326 / Actual pixel size: 1.397 Å
Magnification calibration: CROSS- -CORRELATION DENSITIES WITHIN PROCAPSID SHELL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2364. (DEPOSITION ID: 11635).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 4K7H

4k7h


Accession code: 4K7H / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.4 Å
Refinement stepCycle: LAST / Highest resolution: 4.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11840 0 0 0 11840

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