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- PDB-5j7o: Faustovirus major capsid protein -

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Basic information

Entry
Database: PDB / ID: 5j7o
TitleFaustovirus major capsid protein
Components
  • major capsid protein
  • unknown
KeywordsVIRAL PROTEIN / virus / capsid / double jelly-roll
Function / homologyGroup II dsDNA virus coat/capsid protein / Putative major capsid protein p72
Function and homology information
Biological speciesFaustovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKlose, T. / Rossmann, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Structure of faustovirus, a large dsDNA virus.
Authors: Thomas Klose / Dorine G Reteno / Samia Benamar / Adam Hollerbach / Philippe Colson / Bernard La Scola / Michael G Rossmann /
Abstract: Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that ...Many viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that has been found to use two protein shells to encapsidate and protect its genome. The crystal structure of the major capsid protein, in combination with cryo-electron microscopy structures of two different maturation stages of the virus, shows that the outer virus shell is composed of a double jelly-roll protein that can be found in many double-stranded DNA viruses. The structure of the repeating hexameric unit of the inner shell is different from all other known capsid proteins. In addition to the unique architecture, the region of the genome that encodes the major capsid protein stretches over 17,000 bp and contains a large number of introns and exons. This complexity might help the virus to rapidly adapt to new environments or hosts.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: major capsid protein
B: major capsid protein
C: major capsid protein
D: major capsid protein
E: major capsid protein
F: major capsid protein
G: unknown
H: unknown
I: unknown
J: unknown
K: unknown
L: unknown


Theoretical massNumber of molelcules
Total (without water)441,52312
Polymers441,52312
Non-polymers00
Water23,2751292
1
A: major capsid protein
B: major capsid protein
C: major capsid protein
G: unknown
H: unknown
I: unknown


Theoretical massNumber of molelcules
Total (without water)220,7616
Polymers220,7616
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41230 Å2
ΔGint-271 kcal/mol
Surface area63720 Å2
MethodPISA
2
D: major capsid protein
E: major capsid protein
F: major capsid protein
J: unknown
K: unknown
L: unknown


Theoretical massNumber of molelcules
Total (without water)220,7616
Polymers220,7616
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41110 Å2
ΔGint-278 kcal/mol
Surface area63490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.330, 390.650, 79.490
Angle α, β, γ (deg.)90.00, 112.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
major capsid protein


Mass: 71781.891 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Faustovirus / References: UniProt: A0A0H3TLP8*PLUS
#2: Protein/peptide
unknown


Mass: 1805.216 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Faustovirus
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1292 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M ammonium sulfate, 10% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.37→70.07 Å / Num. obs: 157075 / % possible obs: 89.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.229 / Net I/σ(I): 10.5
Reflection shellResolution: 2.37→2.43 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M3Y

1m3y
PDB Unreleased entry


Resolution: 2.37→70.07 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.22
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 7639 4.87 %Random selection
Rwork0.2034 149347 --
obs0.2056 156977 89.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.37→70.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29592 0 0 1292 30884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330284
X-RAY DIFFRACTIONf_angle_d0.53441388
X-RAY DIFFRACTIONf_dihedral_angle_d14.89310708
X-RAY DIFFRACTIONf_chiral_restr0.0434786
X-RAY DIFFRACTIONf_plane_restr0.0045350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.39690.35392390.31184559X-RAY DIFFRACTION82
2.3969-2.42510.34232380.30724508X-RAY DIFFRACTION82
2.4251-2.45470.3222270.30354519X-RAY DIFFRACTION82
2.4547-2.48580.37392380.3074570X-RAY DIFFRACTION81
2.4858-2.51850.33322420.29774417X-RAY DIFFRACTION82
2.5185-2.5530.31072450.29244555X-RAY DIFFRACTION81
2.553-2.58950.33152390.28884438X-RAY DIFFRACTION81
2.5895-2.62810.3442170.28614501X-RAY DIFFRACTION81
2.6281-2.66920.30842060.29724389X-RAY DIFFRACTION79
2.6692-2.7130.35772410.2814437X-RAY DIFFRACTION81
2.713-2.75970.32170.27614285X-RAY DIFFRACTION77
2.7597-2.80990.32842230.27424464X-RAY DIFFRACTION81
2.8099-2.8640.32322200.26114481X-RAY DIFFRACTION80
2.864-2.92240.31242360.25614479X-RAY DIFFRACTION82
2.9224-2.9860.27042130.25514479X-RAY DIFFRACTION80
2.986-3.05540.29622450.25925072X-RAY DIFFRACTION91
3.0554-3.13180.30292880.24495464X-RAY DIFFRACTION100
3.1318-3.21650.29553090.23765538X-RAY DIFFRACTION100
3.2165-3.31120.26162940.22125496X-RAY DIFFRACTION100
3.3112-3.4180.24032810.21365508X-RAY DIFFRACTION100
3.418-3.54020.24982720.20325500X-RAY DIFFRACTION100
3.5402-3.68190.2582990.19575568X-RAY DIFFRACTION100
3.6819-3.84950.21523040.1795479X-RAY DIFFRACTION100
3.8495-4.05240.22192930.17325501X-RAY DIFFRACTION100
4.0524-4.30630.19532610.15425544X-RAY DIFFRACTION99
4.3063-4.63870.1852570.14385527X-RAY DIFFRACTION99
4.6387-5.10540.1962990.14465513X-RAY DIFFRACTION99
5.1054-5.84390.21962590.16095512X-RAY DIFFRACTION99
5.8439-7.36140.21872550.18095552X-RAY DIFFRACTION99
7.3614-70.10530.18872820.16825483X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29390.0444-0.00560.46540.060.31870.0331-0.0756-0.05910.0216-0.0048-0.050.00250.0837-0.0350.20720.0043-0.0080.27980.00450.375429.357144.518951.5665
20.30560.0822-0.02510.41420.04740.36560.0156-0.04660.0002-0.0458-0.0276-0.0338-0.05180.06670.00770.23590.0149-0.01780.2684-0.01420.37529.680257.880532.5131
30.37860.05040.10150.41110.1010.35910.0131-0.05340.0640.0115-0.03980.062-0.0373-0.0290.03760.20980.0067-0.0060.2408-0.02060.375310.613856.931945.3057
40.51560.080.120.61450.2140.6481-0.00350.0687-0.0587-0.01860.0357-0.07360.10640.0395-0.03820.2309-0.05120.05650.2961-0.0370.303125.4315136.311533.7006
50.19670.0345-0.0150.4490.15650.5769-0.01690.0121-0.0430.0051-0.02340.05970.1246-0.14740.04920.3173-0.07660.07870.3938-0.06040.40833.8281137.736442.7859
60.3717-0.02940.04450.3610.18960.5532-0.01740.0821-0.0189-0.0928-0.01610.0529-0.009-0.09080.03520.2395-0.06170.0410.2967-0.03970.33219.1517149.895923.3873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 621)
2X-RAY DIFFRACTION2chain 'B' and (resid 6 through 621 )
3X-RAY DIFFRACTION3chain 'C' and (resid 6 through 620 )
4X-RAY DIFFRACTION4chain 'D' and (resid 12 through 620)
5X-RAY DIFFRACTION5chain 'E' and (resid 9 through 619)
6X-RAY DIFFRACTION6chain 'F' and (resid 9 through 626)

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