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- PDB-3j31: Life in the extremes: atomic structure of Sulfolobus Turreted Ico... -

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Basic information

Entry
Database: PDB / ID: 3j31
TitleLife in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus
Components
  • A223 penton base
  • A55 membrane protein
  • C381 turret protein
  • Coat protein
KeywordsVIRUS / Virus assembly / Evolution / Archaea
Function / homology
Function and homology information


: / : / : / : / C381 turret protein 2nd galactose-binding domain-like / C381 turret protein 1st galactose-binding domain-like / C381 turret protein Nucleoplasmin-like/VP domain / Sulfolobus turreted icosahedral virus 1-like, major capsid protein / : / A223 penton protein second domain
Similarity search - Domain/homology
Coat protein / Uncharacterized protein / A223 penton protein C-terminal domain-containing protein
Similarity search - Component
Biological speciesSulfolobus turreted icosahedral virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsVeesler, D. / Ng, T.S. / Sendamarai, A.K. / Eilers, B.J. / Lawrence, C.M. / Lok, S.M. / Young, M.J. / Johnson, J.E. / Fu, C.-Y.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography.
Authors: David Veesler / Thiam-Seng Ng / Anoop K Sendamarai / Brian J Eilers / C Martin Lawrence / Shee-Mei Lok / Mark J Young / John E Johnson / Chi-yu Fu /
Abstract: Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution ...Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution electron microscopy and X-ray crystallography allowing tracing of structural polypeptide chains and visualization of transmembrane proteins embedded in the viral membrane. We propose that the vertex complexes orchestrate virion assembly by coordinating interactions of the membrane and various protein components involved. STIV shares the same coat subunit and penton base protein folds as some eukaryotic and bacterial viruses, suggesting that they derive from a common ancestor predating the divergence of the three kingdoms of life. One architectural motif (β-jelly roll fold) forms virtually the entire capsid (distributed in three different gene products), indicating that a single ancestral protein module may have been at the origin of its evolution.
History
DepositionFeb 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Feb 21, 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-5584
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  • Superimposition on EM map
  • EMDB-5584
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Q: A223 penton base
R: A55 membrane protein
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: C381 turret protein


Theoretical massNumber of molelcules
Total (without water)635,32318
Polymers635,32318
Non-polymers00
Water00
1
Q: A223 penton base
R: A55 membrane protein
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: C381 turret protein
x 60


Theoretical massNumber of molelcules
Total (without water)38,119,3841080
Polymers38,119,3841080
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
Q: A223 penton base
R: A55 membrane protein
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: C381 turret protein
x 5


  • icosahedral pentamer
  • 3.18 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)3,176,61590
Polymers3,176,61590
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
Q: A223 penton base
R: A55 membrane protein
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: C381 turret protein
x 6


  • icosahedral 23 hexamer
  • 3.81 MDa, 108 polymers
Theoretical massNumber of molelcules
Total (without water)3,811,938108
Polymers3,811,938108
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))

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Components

#1: Protein A223 penton base


Mass: 24439.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus turreted icosahedral virus / References: UniProt: Q6Q0L4
#2: Protein/peptide A55 membrane protein


Mass: 1294.587 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Sulfolobus turreted icosahedral virus
#3: Protein
Coat protein / B345 coat subunit


Mass: 37858.805 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Sulfolobus turreted icosahedral virus / References: UniProt: Q6Q0J0
#4: Protein C381 turret protein


Mass: 41706.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus turreted icosahedral virus / References: UniProt: Q6Q0L3
Sequence detailsCHAIN R CORRESPONDS TO A PORTION OF THE SEQUENCE ...CHAIN R CORRESPONDS TO A PORTION OF THE SEQUENCE MNIEEIQYEVGQEDQIPPAQTKTVVVQQNPKLFGISVWIWIIIILVLILLVLIIK (UNP Q6Q0M0).

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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: Mature Sulfolobus Turreted Icosahedral Virus / Type: VIRUS
Molecular weightValue: 75 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: YES / Host category: ARCHAEA / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Sulfolobus solfataricus
Buffer solutionName: 23 mM KH2PO4, 19 mM (NH4)2SO4, 1 mM MgSO4, 2 mM CaCl2 / pH: 3.5
Details: 23 mM KH2PO4, 19 mM (NH4)2SO4, 1 mM MgSO4, 2 mM CaCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged C-flat holey carbon grids (CF-2/2-4C, Protochips)
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 94 K
Details: Vitrification carried out at room temperature using liquid ethane and a homemade plunger

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 30, 2011 / Details: Nanoprobe mode was used.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 102189 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 103000 times magnification
Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen holder type: Nitrogen cooled / Temperature: 90 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 18 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k) / Details: Non-backthinned chip
Image scansNum. digital images: 878
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1CNSmodel fitting
2FREALIGN3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Projection matching / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8903 / Actual pixel size: 1.37 Å / Magnification calibration: Fitting of atomic coordinates
Details: The final reconstruction was sharpened with a negative temperature factor of 400A2 (Single particle--Applied symmetry: I) Resolution method was FSC at 0.143 cut-off. The reported resolution ...Details: The final reconstruction was sharpened with a negative temperature factor of 400A2 (Single particle--Applied symmetry: I) Resolution method was FSC at 0.143 cut-off. The reported resolution is for the entire reconstruction. The resolution of the coat subunit region (B345) is estimated to 3.9 A using the same criterion.
Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITRECIPROCALREFINEMENT PROTOCOL--positional (xyz) minimization and isotropic B factor refinement DETAILS--Real space refinement was also carried out using Coot.
2FLEXIBLE FITRECIPROCALREFINEMENT PROTOCOL--positional (xyz) minimization and isotropic B factor refinement DETAILS--Real space refinement was also carried out using Coot. Only the N-terminal domain was refined using CNS (residues 3-134). The C-terminal domain (residues 135-222) was only rigid-body fit using Coot and an arbitrary B-factor value of 150 A2 was assigned to it.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12BBD

2bbd

12BBD1PDBexperimental model
24IL7

4il7

24IL72PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms44549 0 0 0 44549

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