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- PDB-6c3r: Cricket paralysis virus RNAi suppressor protein CrPV-1A -

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Basic information

Entry
Database: PDB / ID: 6c3r
TitleCricket paralysis virus RNAi suppressor protein CrPV-1A
ComponentsCricket paralysis virus 1A protein
KeywordsVIRAL PROTEIN / RNAi inhibitor
Function / homology
Function and homology information


negative regulation of endoribonuclease activity / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / Cul2-RING ubiquitin ligase complex / endoribonuclease inhibitor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / protein ubiquitination / RNA-directed RNA polymerase / viral RNA genome replication ...negative regulation of endoribonuclease activity / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / Cul2-RING ubiquitin ligase complex / endoribonuclease inhibitor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / protein ubiquitination / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / ATP binding
Similarity search - Function
Peptidase C3G, Picornavirus / Tungro spherical virus-type peptidase / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / RNA-directed RNA polymerase, C-terminal domain ...Peptidase C3G, Picornavirus / Tungro spherical virus-type peptidase / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Replicase polyprotein
Similarity search - Component
Biological speciesCricket paralysis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsNayak, A. / Kim, D.Y. / Andino, R. / Gross, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI36178, AI40085 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI091575 United States
Department of Defense (DOD, United States)DARPA Prophecy United States
CitationJournal: Cell Host Microbe / Year: 2018
Title: A Viral Protein Restricts Drosophila RNAi Immunity by Regulating Argonaute Activity and Stability.
Authors: Nayak, A. / Kim, D.Y. / Trnka, M.J. / Kerr, C.H. / Lidsky, P.V. / Stanley, D.J. / Rivera, B.M. / Li, K.H. / Burlingame, A.L. / Jan, E. / Frydman, J. / Gross, J.D. / Andino, R.
History
DepositionJan 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cricket paralysis virus 1A protein
B: Cricket paralysis virus 1A protein


Theoretical massNumber of molelcules
Total (without water)33,5842
Polymers33,5842
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-12 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.854, 52.117, 111.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cricket paralysis virus 1A protein


Mass: 16791.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricket paralysis virus / Gene: ORF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9IJX4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: PEG 3350 Lithium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 9872 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.082 / Χ2: 1.475 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.6-2.644.80.9174791.2881100
2.64-2.694.80.7784701.341100
2.69-2.744.70.7064941.3611100
2.74-2.84.70.6194711.4771100
2.8-2.864.80.5694811.4841100
2.86-2.934.70.4264951.4751100
2.93-34.70.3284691.5011100
3-3.084.70.2795061.4411100
3.08-3.174.80.2344701.4861100
3.17-3.284.80.1864891.441100
3.28-3.394.70.1354721.471100
3.39-3.534.70.1015121.3421100
3.53-3.694.70.0864901.4321100
3.69-3.884.70.0634771.3461100
3.88-4.124.70.0565061.3341100
4.12-4.444.70.0454901.5391100
4.44-4.894.60.0415081.7181100
4.89-5.594.50.0465092.0081100
5.59-7.034.30.0435151.6491100
7.03-304.20.0255691.391100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.884 / SU B: 30.619 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 467 4.8 %RANDOM
Rwork0.2189 ---
obs0.2218 9252 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 144.83 Å2 / Biso mean: 57.688 Å2 / Biso min: 22.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.89 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 0 25 2387
Biso mean---39.43 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192429
X-RAY DIFFRACTIONr_bond_other_d0.0020.022186
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9343278
X-RAY DIFFRACTIONr_angle_other_deg0.91335024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63124.143140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05115416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7271516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 35 -
Rwork0.292 638 -
all-673 -
obs--99.41 %
Refinement TLS params.Method: refined / Origin x: 52.7523 Å / Origin y: -9.3304 Å / Origin z: 59.4187 Å
111213212223313233
T0.0242 Å2-0.0179 Å20.0194 Å2-0.131 Å2-0.0158 Å2--0.0622 Å2
L0.3425 °2-0.3023 °20.3744 °2-1.317 °2-1.273 °2--1.5073 °2
S0.0193 Å °0.1062 Å °-0.0317 Å °0.0967 Å °-0.0394 Å °0.0832 Å °-0.0768 Å °0.1336 Å °0.0201 Å °

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