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- PDB-4i1t: Crystal structure of the cap-snatching endonuclease from Pichinde... -

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Basic information

Entry
Database: PDB / ID: 4i1t
TitleCrystal structure of the cap-snatching endonuclease from Pichinde virus
ComponentsRNA-directed RNA polymerase L
KeywordsVIRAL PROTEIN / Arenavirus / Pichinde virus / viral transcription / cap-snatching / endonuclease / L protein / RNA-dependent RNA polymerase / PD-(D/E)XK nuclease fold / cap-snatching RNA endonuclease
Function / homology
Function and homology information


cap snatching / virion component / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase L, helical domain / Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / de novo design (two linked rop proteins) / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. ...RNA-directed RNA polymerase L, helical domain / Arenavirus RNA polymerase / RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / de novo design (two linked rop proteins) / : / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesPichinde virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBussetta, C. / Choi, K.H.
CitationJournal: To be Published
Title: Crystal structure of the cap-snatching endonuclease from Pichinde virus, a new world arenavirus
Authors: Bussetta, C. / Ye, M. / Shrestha, L. / Bujalowski, P.J. / White, M.A. / Choi, K.H.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)25,1411
Polymers25,1411
Non-polymers00
Water00
1
A: RNA-directed RNA polymerase L

A: RNA-directed RNA polymerase L


Theoretical massNumber of molelcules
Total (without water)50,2822
Polymers50,2822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.962, 142.962, 46.835
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L


Mass: 25140.799 Da / Num. of mol.: 1
Fragment: cap-snatching endonuclease domain (residues 1-194)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pichinde virus / Strain: AN3739 / Gene: L / Plasmid: pJexpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q915A5, RNA-directed RNA polymerase

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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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 6M ammonium nitrate, 0.1M Tris, pH 8.5, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 9, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 7360 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Rmerge(I) obs: 0.088 / Χ2: 1.896 / Net I/σ(I): 29.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.8-2.853.90.623.773501.48797.8
2.85-2.94.60.882.133481.67498.9
2.9-2.965.20.8042.093661.46100
2.96-3.025.90.82.433461.51100
3.02-3.086.40.6094.033581.97399.7
3.08-3.157.90.55.973621.795100
3.15-3.239.50.4028.383611.749100
3.23-3.329.70.311.93591.872100
3.32-3.429.80.26913.73611.961100
3.42-3.539.90.21916.93502.093100
3.53-3.6510.50.18420.123741.971100
3.65-3.8110.15124.473591.973100
3.8-3.97110.12928.883712.182100
3.97-4.1824.70.13642.563651.856100
4.18-4.4427.60.10857.073672.03100
4.44-4.7928.10.08569.023751.878100
4.79-5.2728.80.08569.033791.923100
5.27-6.0328.60.09365.073791.886100
6.03-7.5928.20.06583.243911.751100
7.59-5024.50.03997.814391.971100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å46.8 Å
Translation4 Å46.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JSB

3jsb


Resolution: 2.8→46.795 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 339 4.65 %RANDOM
Rwork0.2361 ---
obs0.2387 7286 99.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.042 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso max: 185.25 Å2 / Biso mean: 78.3406 Å2 / Biso min: 24.96 Å2
Baniso -1Baniso -2Baniso -3
1-6.7793 Å20 Å2-0 Å2
2--6.7793 Å20 Å2
3----13.5585 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 0 0 1386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091411
X-RAY DIFFRACTIONf_angle_d1.2081907
X-RAY DIFFRACTIONf_chiral_restr0.073220
X-RAY DIFFRACTIONf_plane_restr0.005237
X-RAY DIFFRACTIONf_dihedral_angle_d17.223543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.8001-3.52770.34021830.256334735303347
3.5277-46.80180.27451560.2293360037563600
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)
12.5227-2.49550.43013.3863-0.59952.0962-0.24470.14390.96-0.45140.02520.2786-0.2925-0.4684-0.00460.21680.04320.07120.78030.00790.451-1.182351.882510.7352
23.74110.812-1.83681.30330.14242.40170.01310.55180.1024-0.48790.1750.843-0.1678-1.05310.01260.13890.27990.03280.6888-0.01780.394720.926355.16080.9836
31.6564-0.1682-0.92170.92820.45872.3489-0.6320.9031-0.7456-0.8310.22020.11761.0736-0.15530.00450.42230.13560.13330.5871-0.13270.500124.98943.7097-3.4033
41.7572-1.1973-0.80931.6333-1.18783.5546-0.1001-0.8494-0.66780.03910.40270.48591.5649-0.34040.0554-0.0691-0.00310.06870.59330.05720.4698.614343.24112.0863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:50)A1 - 50
2X-RAY DIFFRACTION2(chain A and resid 51:106)A51 - 106
3X-RAY DIFFRACTION3(chain A and resid 107:133)A107 - 133
4X-RAY DIFFRACTION4(chain A and resid 134:169)A134 - 169

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