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- PDB-4nww: Crystal structure of an N-terminally truncated capsid protein mut... -

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Basic information

Entry
Database: PDB / ID: 4nww
TitleCrystal structure of an N-terminally truncated capsid protein mutant of Orsay virus
ComponentsCapsid proteinCapsid
KeywordsVIRUS / beta barrel
Function / homologyNodavirus capsid / nodavirus capsid protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Capsid protein alpha
Function and homology information
Biological speciesOrsay nodavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.75 Å
AuthorsTao, Y.J. / Guo, Y.R.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Crystal structure of a nematode-infecting virus.
Authors: Yusong R Guo / Corey F Hryc / Joanita Jakana / Hongbing Jiang / David Wang / Wah Chiu / Weiwei Zhong / Yizhi J Tao /
Abstract: Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, ...Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid-δ fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, β-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references / Derived calculations
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3156
Polymers118,1953
Non-polymers1203
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)7,098,900360
Polymers7,091,686180
Non-polymers7,214180
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 592 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)591,57530
Polymers590,97415
Non-polymers60115
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 710 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)709,89036
Polymers709,16918
Non-polymers72118
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 60
A: Capsid protein
B: Capsid protein
C: Capsid protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 14.2 MDa, 360 polymers
Theoretical massNumber of molelcules
Total (without water)14,197,800720
Polymers14,183,371360
Non-polymers14,428360
Water0
TypeNameSymmetry operationNumber
transform to crystal frame2
point symmetry operation120
Unit cell
Length a, b, c (Å)404.921, 375.148, 412.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.809017, -0.5, 0.30901699), (0.5, 0.309017, -0.80901699), (0.30901699, 0.80901699, 0.5)
3generate(0.5, -0.309017, 0.80901699), (0.309017, -0.80901699, -0.5), (0.80901699, 0.5, -0.309017)
4generate(0.5, 0.30901699, 0.809017), (-0.30901699, -0.809017, 0.5), (0.80901699, -0.5, -0.30901699)
5generate(0.80901699, 0.5, 0.309017), (-0.5, 0.30901699, 0.80901699), (0.30901699, -0.809017, 0.5)
6generate(-0.5, 0.30901699, 0.80901699), (0.309017, -0.80901699, 0.50000001), (0.809017, 0.49999999, 0.30901699)
7generate(1), (1), (1)
8generate(0.5, 0.309017, -0.80901699), (0.309017, 0.80901699, 0.5), (0.80901699, -0.5, 0.309017)
9generate(0.309017, -0.80901699, -0.5), (0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.809017)
10generate(-0.30901699, -0.809017, 0.5), (0.809017, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699)
11generate(-0.309017, 0.80901699, -0.50000001), (-0.809017, -0.49999999, -0.30901699), (-0.5, 0.30901699, 0.80901699)
12generate(-1), (-1), (1)
13generate(-0.309017, -0.80901699, -0.5), (-0.80901699, 0.5, -0.309017), (0.5, 0.309017, -0.80901699)
14generate(-0.80901699, -0.5, 0.30901699), (-0.5, 0.30901699, -0.809017), (0.309017, -0.80901699, -0.5)
15generate(-0.809017, 0.5, 0.30901699), (-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.809017, 0.5)
DetailsT=3 icosahedral symmetry. The deposited coordinates represent 1 icosahedral asymmetric unit. The crystal asymmetric unit is 15-meric. The biological assembly is an icosahedron. The complete crystal unit cell contains 2 icosahedral virus particles.

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Components

#1: Protein Capsid protein / Capsid


Mass: 39398.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orsay nodavirus / Gene: Capsid Protein / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: E9KNV5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.7-1.05 M sodium malonate, 0.25%-1% (v/v) Jeffamine ED-2001, 0.1 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.75→30 Å / Num. obs: 204023 / % possible obs: 64.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.247 / Net I/σ(I): 2.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.75-3.811.80.668168
3.81-3.881.80.614167.6
3.88-3.961.90.601167.4
3.96-4.041.90.485167.4
4.04-4.131.90.438167.1
4.13-4.221.90.418166.8
4.22-4.331.90.337166.6
4.33-4.441.90.284166.2
4.44-4.571.90.257166
4.57-4.721.90.243165.3
4.72-4.891.90.229165.3
4.89-5.081.90.229164.6
5.08-5.311.90.235164.2
5.31-5.5920.222163.8
5.59-5.9420.248163.1
5.94-6.420.212162.4
6.4-7.0320.177161.6
7.03-8.0320.137160.6
8.03-10.062.10.087158.7
10.06-302.10.052154.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_RNP

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
CNSrefinement
PDB_EXTRACT3.11data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 3.75→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3008 10134 3.2 %
Rwork0.2988 193341 -
obs-203475 64.2 %
Solvent computationBsol: 24.4537 Å2
Displacement parametersBiso max: 200 Å2 / Biso mean: 68.4005 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1--13.704 Å20 Å20 Å2
2--26.115 Å20 Å2
3----12.412 Å2
Refinement stepCycle: LAST / Resolution: 3.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8016 0 3 0 8019

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