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- PDB-3jb1: Atomic model of cytoplasmic polyhedrosis virus with SAM -

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Basic information

Entry
Database: PDB / ID: 3jb1
TitleAtomic model of cytoplasmic polyhedrosis virus with SAM
Components
  • Capsid protein VP1
  • Structural protein VP3
  • Viral structural protein 5
KeywordsVIRUS / viral ATPase / histidine-mediated guanylyl transfer / conformational changes / regulation of transcription
Function / homology
Function and homology information


T=2 icosahedral viral capsid / viral inner capsid
Similarity search - Function
: / Viral structural protein 5 / : / CPV Capsid shell protein VP1, small protrusion domain / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain ...: / Viral structural protein 5 / : / CPV Capsid shell protein VP1, small protrusion domain / : / : / : / : / Reovirus VP3 protein, guanylyltransferase (GTase) / Reovirus turret protein, bridge domain / Reovirus VP3 protein, Methyltransferase domain 1 / Reovirus VP3 protein, Methyltransferase domain 2 / : / Inner layer core protein VP1-like, C-terminal
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Viral structural protein 5 / Inner capsid protein VP1 / Structural protein VP3
Similarity search - Component
Biological speciesBombyx mori cypovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYu, X.K. / Jiang, J.S. / Sun, J.C. / Zhou, Z.H.
CitationJournal: Elife / Year: 2015
Title: A putative ATPase mediates RNA transcription and capping in a dsRNA virus.
Authors: Xuekui Yu / Jiansen Jiang / Jingchen Sun / Z Hong Zhou /
Abstract: mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high- ...mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high-resolution (2.9-3.1 Å) cryo-electron microscopy structures of cytoplasmic polyhedrosis virus with bound ligands, we show that the large sub-domain of the guanylyltransferase (GTase) domain of the turret protein (TP) also has an ATP-binding site and is likely an ATPase. S-adenosyl-L-methionine (SAM) acts as a signal and binds the methylase-2 domain of TP to induce conformational change of the viral capsid, which in turn activates the putative ATPase. ATP binding/hydrolysis leads to an enlarged capsid for efficient mRNA synthesis, an open GTase domain for His217-mediated guanylyl transfer, and an open methylase-1 domain for SAM binding and methyl transfer. Taken together, our data support a role of the putative ATPase in mediating the activation of mRNA transcription and capping within the confines of the virus.
History
DepositionJul 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)517,4786
Polymers517,0805
Non-polymers3981
Water00
1
A: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)31,048,698360
Polymers31,024,792300
Non-polymers23,90660
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: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5
hetero molecules
x 5


  • icosahedral pentamer
  • 2.59 MDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)2,587,39230
Polymers2,585,39925
Non-polymers1,9925
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Structural protein VP3
B: Capsid protein VP1
C: Capsid protein VP1
D: Viral structural protein 5
E: Viral structural protein 5
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 3.1 MDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)3,104,87036
Polymers3,102,47930
Non-polymers2,3916
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))

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Components

#1: Protein Structural protein VP3 / TP


Mass: 120145.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q914N6
#2: Protein Capsid protein VP1 / CSP-A and CSP-B


Mass: 148560.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q6TS43
#3: Protein Viral structural protein 5 / LPP-3 and LPP-5


Mass: 49906.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: C6K2M8
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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

Component
IDNameTypeDetailsParent-ID
1Cytoplasmic polyhedrosis virus with SAMVIRUSicosahedral0
2Bombyx mori cypovirus 1VIRUS1
Details of virusEmpty: NO / Enveloped: NO / Host category: INVERTEBRATES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Bombyx mori
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK II)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 8, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 60535 X / Cs: 2.75 mm
Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification.
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: IMIRS / Category: 3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Cross-common lines / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44908 / Nominal pixel size: 1.104 Å / Actual pixel size: 1.104 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
RefinementResolution: 3.1→39.032 Å / SU ML: 0.57 / σ(F): 2 / Phase error: 27.67 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.202 1703 0.23 %
Rwork0.1985 754568 -
obs0.1985 756271 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 530.97 Å2 / Biso mean: 204.9893 Å2 / Biso min: 126.4 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32244 0 27 0 32271
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00632945
ELECTRON MICROSCOPYf_angle_d1.07444854
ELECTRON MICROSCOPYf_chiral_restr0.0745180
ELECTRON MICROSCOPYf_plane_restr0.0055830
ELECTRON MICROSCOPYf_dihedral_angle_d15.00212129
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.19120.49561680.49886278262950
3.1912-3.29420.44591440.45536338763531
3.2942-3.41180.39711440.39966247062614
3.4118-3.54840.33591440.33936309263236
3.5484-3.70970.24011440.27156267562819
3.7097-3.90510.22881320.20826308463216
3.9051-4.14960.16471440.15526293663080
4.1496-4.46950.13661320.12536300263134
4.4695-4.91850.13631320.13536273162863
4.9185-5.62840.17361560.18026291863074
5.6284-7.08430.2086960.21786279762893
7.0843-39.03540.19851670.18166269462861
Refinement TLS params.Method: refined / Origin x: -42.333 Å / Origin y: -68.136 Å / Origin z: 259.7022 Å
111213212223313233
T1.7148 Å2-0.0166 Å20.021 Å2-1.6309 Å20.0519 Å2--1.6925 Å2
L0.2534 °2-0.0691 °20.0015 °2-0.0495 °2-0.0338 °2--0.0262 °2
S-0.0119 Å °-0.0023 Å °0.1927 Å °-0.0173 Å °-0.0012 Å °-0.1 Å °-0.0663 Å °0.0271 Å °0.0131 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1ELECTRON MICROSCOPY1allA1 - 1057
2ELECTRON MICROSCOPY1allB135 - 1333
3ELECTRON MICROSCOPY1allC74 - 1333
4ELECTRON MICROSCOPY1allD1 - 292
5ELECTRON MICROSCOPY1allE1 - 292
6ELECTRON MICROSCOPY1allA0 - 1101

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